Comments (34)
goldenflaw
commented on September 19, 2024
Could you send us your leafcutter output file?
Best,
Yang
…On Thu, Mar 8, 2018 at 9:22 AM, seyfim ***@***.***> wrote:
within my data I only have 3 replicates per sample so there are 6 total
samples in a comparison. I am able to generate the
leafcutter_ds_effect_size.txt and leafcutter_ds_cluster_significance.txt
files but when I use them in the prepare_results.R script for visualization
I get the following error:Error: No significant clusters found
However, I have been using other alternative splicing tools like rMATS,
MISO and SUPPA and I get 100's of significant calls. So I was wondering if
my small sample size is to blame for no significant cluster detection?
—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
<#56>, or mute the
thread
<https://github.com/notifications/unsubscribe-auth/AE1pif_sDRFUWAqaWL3PMjcEzD9ZXrAJks5tcUyogaJpZM4Si2YZ>
.
from leafcutter.
seyfim
commented on September 19, 2024
leafcutter_ds_cluster_significance.txt
leafcutter_ds_effect_sizes.txt
@goldenflaw
from leafcutter.
goldenflaw
commented on September 19, 2024
I think the output looks fine, so it could be that LeafCutter was not able
to find any significant hit. I am very surprised that other programs are
able to get many hits. Could you make sure that you believe the output from
the other tools? If so, I will gladly try to investigate why LeafCutter is
not finding those.
Best,
Yang
…On Thu, Mar 8, 2018 at 9:51 AM, seyfim ***@***.***> wrote:
leafcutter_ds_cluster_significance.txt
<https://github.com/davidaknowles/leafcutter/files/1793767/leafcutter_ds_cluster_significance.txt>
leafcutter_ds_effect_sizes.txt
<https://github.com/davidaknowles/leafcutter/files/1793768/leafcutter_ds_effect_sizes.txt>
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#56 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AE1piYhwtmePPGrise8-cvP_Nl-X6ch8ks5tcVNxgaJpZM4Si2YZ>
.
from leafcutter.
mh406910
commented on September 19, 2024
I am very confident in my outputs from the other programs. We get so many hits that we typically filter the significant splicing based on FDR of 0.01 and then we check out the distribution of delta psi with violin plots to assess a cutoff. I was shocked that an FDR of 0.05 showed no hits with your software. It would be great if you could investigate! @goldenflaw
from leafcutter.
goldenflaw
commented on September 19, 2024
Would it be convenient for you to send us your data? Perhaps 1 chromosome.
Best,
Yang
…On Thu, Mar 8, 2018 at 11:09 AM, mh406910 ***@***.***> wrote:
I am very confident in my outputs from the other programs. We get so many
hits that we typically filter the significant splicing based on FDR of 0.01
and then we check out the distribution of delta psi with violin plots to
assess a cutoff. I was shocked that an FDR of 0.05 showed no hits with your
software. It would be great if you could investigate!
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#56 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AE1pieTQQNQ06Xc9Ed9BiNT8J0sTVbl9ks5tcWXDgaJpZM4Si2YZ>
.
from leafcutter.
seyfim
commented on September 19, 2024
test_perind.counts.gz
test_perind_numers.counts.gz
P14WtMut.txt
leafcutter_ds_cluster_significance.txt
leafcutter_ds_effect_sizes.txt
mm10_ens.txt.gz
@goldenflaw
from leafcutter.
seyfim
commented on September 19, 2024
how do I just share one chromosome with you? @goldenflaw
from leafcutter.
goldenflaw
commented on September 19, 2024
I will have a look at the whole thing.
Best,
Yang
…On Mar 9, 2018 8:54 AM, "seyfim" ***@***.***> wrote:
how do I just share one chromosome with you?
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#56 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AE1piZqBGBpzf2cNNshOQCmtkfMdzzChks5tcpe2gaJpZM4Si2YZ>
.
from leafcutter.
goldenflaw
commented on September 19, 2024
Your P14WTmut.txt file looks wrong, you only have 2 samples in there.
Best,
Yang
…On Fri, Mar 9, 2018 at 9:07 AM, Yang Li ***@***.***> wrote:
I will have a look at the whole thing.
Best,
Yang
On Mar 9, 2018 8:54 AM, "seyfim" ***@***.***> wrote:
> how do I just share one chromosome with you?
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <#56 (comment)>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AE1piZqBGBpzf2cNNshOQCmtkfMdzzChks5tcpe2gaJpZM4Si2YZ>
> .
>
from leafcutter.
mh406910
commented on September 19, 2024
Those are merged ban files of the. 3X replicates per sample
Get Outlook for Android<https://aka.ms/ghei36>
________________________________
From: goldenflaw <[email protected]>
Sent: Tuesday, March 13, 2018 3:02:47 PM
To: davidaknowles/leafcutter
Cc: Seyfi, Marilyn; Comment
Subject: Re: [davidaknowles/leafcutter] small sample size affecting cluster significance detection? (#56)
Your P14WTmut.txt file looks wrong, you only have 2 samples in there.
Best,
Yang
On Fri, Mar 9, 2018 at 9:07 AM, Yang Li ***@***.***> wrote:
I will have a look at the whole thing.
Best,
Yang
On Mar 9, 2018 8:54 AM, "seyfim" ***@***.***> wrote:
> how do I just share one chromosome with you?
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <#56 (comment)>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AE1piZqBGBpzf2cNNshOQCmtkfMdzzChks5tcpe2gaJpZM4Si2YZ>
> .
>
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub<#56 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AH0qV7HiNDq4nRYq6MBi9a1xWDnMNfEUks5teBfWgaJpZM4Si2YZ>.
from leafcutter.
goldenflaw
commented on September 19, 2024
I would separate them then and run leafcutter again. You cannot estimate
sample variation with 1 sample so I am very surprised you get results from
other tools.
Best,
Yang
…On Tue, Mar 13, 2018 at 5:17 PM, mh406910 ***@***.***> wrote:
Those are merged ban files of the. 3X replicates per sample
Get Outlook for Android<https://aka.ms/ghei36>
________________________________
From: goldenflaw ***@***.***>
Sent: Tuesday, March 13, 2018 3:02:47 PM
To: davidaknowles/leafcutter
Cc: Seyfi, Marilyn; Comment
Subject: Re: [davidaknowles/leafcutter] small sample size affecting
cluster significance detection? (#56)
Your P14WTmut.txt file looks wrong, you only have 2 samples in there.
Best,
Yang
On Fri, Mar 9, 2018 at 9:07 AM, Yang Li ***@***.***> wrote:
> I will have a look at the whole thing.
>
> Best,
> Yang
>
> On Mar 9, 2018 8:54 AM, "seyfim" ***@***.***> wrote:
>
>> how do I just share one chromosome with you?
>>
>> —
>> You are receiving this because you were mentioned.
>> Reply to this email directly, view it on GitHub
>> <#56 (comment)-
371835036>,
>> or mute the thread
>> <https://github.com/notifications/unsubscribe-auth/
AE1piZqBGBpzf2cNNshOQCmtkfMdzzChks5tcpe2gaJpZM4Si2YZ>
>> .
>>
>
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub<https://github.com/
davidaknowles/leafcutter#56#issuecomment-372781944>, or mute the
thread<https://github.com/notifications/unsubscribe-auth/
AH0qV7HiNDq4nRYq6MBi9a1xWDnMNfEUks5teBfWgaJpZM4Si2YZ>.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#56 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AE1piaCs4ooiofNzV_HFFlkwuK5MJ2npks5teEWCgaJpZM4Si2YZ>
.
from leafcutter.
mh406910
commented on September 19, 2024
Also when I run your program with the replicates unmerged as separate replicates I get the same error that there are no significant clusters. MISO and rMATS both report otherwise.
Get Outlook for Android<https://aka.ms/ghei36>
________________________________
From: goldenflaw <[email protected]>
Sent: Tuesday, March 13, 2018 3:02:47 PM
To: davidaknowles/leafcutter
Cc: Seyfi, Marilyn; Comment
Subject: Re: [davidaknowles/leafcutter] small sample size affecting cluster significance detection? (#56)
Your P14WTmut.txt file looks wrong, you only have 2 samples in there.
Best,
Yang
On Fri, Mar 9, 2018 at 9:07 AM, Yang Li ***@***.***> wrote:
I will have a look at the whole thing.
Best,
Yang
On Mar 9, 2018 8:54 AM, "seyfim" ***@***.***> wrote:
> how do I just share one chromosome with you?
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <#56 (comment)>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AE1piZqBGBpzf2cNNshOQCmtkfMdzzChks5tcpe2gaJpZM4Si2YZ>
> .
>
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub<#56 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AH0qV7HiNDq4nRYq6MBi9a1xWDnMNfEUks5teBfWgaJpZM4Si2YZ>.
from leafcutter.
mh406910
commented on September 19, 2024
Miso only takes merged replicate files and,we get significant AS events
Get Outlook for Android<https://aka.ms/ghei36>
________________________________
From: goldenflaw <[email protected]>
Sent: Tuesday, March 13, 2018 6:20:09 PM
To: davidaknowles/leafcutter
Cc: Seyfi, Marilyn; Comment
Subject: Re: [davidaknowles/leafcutter] small sample size affecting cluster significance detection? (#56)
I would separate them then and run leafcutter again. You cannot estimate
sample variation with 1 sample so I am very surprised you get results from
other tools.
Best,
Yang
On Tue, Mar 13, 2018 at 5:17 PM, mh406910 ***@***.***> wrote:
Those are merged ban files of the. 3X replicates per sample
Get Outlook for Android<https://aka.ms/ghei36>
________________________________
From: goldenflaw ***@***.***>
Sent: Tuesday, March 13, 2018 3:02:47 PM
To: davidaknowles/leafcutter
Cc: Seyfi, Marilyn; Comment
Subject: Re: [davidaknowles/leafcutter] small sample size affecting
cluster significance detection? (#56)
Your P14WTmut.txt file looks wrong, you only have 2 samples in there.
Best,
Yang
On Fri, Mar 9, 2018 at 9:07 AM, Yang Li ***@***.***> wrote:
> I will have a look at the whole thing.
>
> Best,
> Yang
>
> On Mar 9, 2018 8:54 AM, "seyfim" ***@***.***> wrote:
>
>> how do I just share one chromosome with you?
>>
>> —
>> You are receiving this because you were mentioned.
>> Reply to this email directly, view it on GitHub
>> <#56 (comment)-
371835036>,
>> or mute the thread
>> <https://github.com/notifications/unsubscribe-auth/
AE1piZqBGBpzf2cNNshOQCmtkfMdzzChks5tcpe2gaJpZM4Si2YZ>
>> .
>>
>
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub<https://github.com/
davidaknowles/leafcutter#56#issuecomment-372781944>, or mute the
thread<https://github.com/notifications/unsubscribe-auth/
AH0qV7HiNDq4nRYq6MBi9a1xWDnMNfEUks5teBfWgaJpZM4Si2YZ>.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#56 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AE1piaCs4ooiofNzV_HFFlkwuK5MJ2npks5teEWCgaJpZM4Si2YZ>
.
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub<#56 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AH0qV0I8R6DN5JfH4HQw-gabStWQ0l4zks5teEYZgaJpZM4Si2YZ>.
from leafcutter.
goldenflaw
commented on September 19, 2024
Could you provide the correct mapping of samples to conditions? And your
strongest "hit" from rMATS and or MISO.
Best,
Yang
…On Tue, Mar 13, 2018 at 5:21 PM, mh406910 ***@***.***> wrote:
Also when I run your program with the replicates unmerged as separate
replicates I get the same error that there are no significant clusters.
MISO and rMATS both report otherwise.
Get Outlook for Android<https://aka.ms/ghei36>
________________________________
From: goldenflaw ***@***.***>
Sent: Tuesday, March 13, 2018 3:02:47 PM
To: davidaknowles/leafcutter
Cc: Seyfi, Marilyn; Comment
Subject: Re: [davidaknowles/leafcutter] small sample size affecting
cluster significance detection? (#56)
Your P14WTmut.txt file looks wrong, you only have 2 samples in there.
Best,
Yang
On Fri, Mar 9, 2018 at 9:07 AM, Yang Li ***@***.***> wrote:
> I will have a look at the whole thing.
>
> Best,
> Yang
>
> On Mar 9, 2018 8:54 AM, "seyfim" ***@***.***> wrote:
>
>> how do I just share one chromosome with you?
>>
>> —
>> You are receiving this because you were mentioned.
>> Reply to this email directly, view it on GitHub
>> <#56 (comment)-
371835036>,
>> or mute the thread
>> <https://github.com/notifications/unsubscribe-auth/
AE1piZqBGBpzf2cNNshOQCmtkfMdzzChks5tcpe2gaJpZM4Si2YZ>
>> .
>>
>
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub<https://github.com/
davidaknowles/leafcutter#56#issuecomment-372781944>, or mute the
thread<https://github.com/notifications/unsubscribe-auth/
AH0qV7HiNDq4nRYq6MBi9a1xWDnMNfEUks5teBfWgaJpZM4Si2YZ>.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#56 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AE1pif2tfb_R056uBWbmrOrB1zLXuxdoks5teEZOgaJpZM4Si2YZ>
.
from leafcutter.
mh406910
commented on September 19, 2024
Just to clarify you mean the ban file? As well as the output from rMATS and MISO with their highest delta pi value for the selected sample comparison?
Get Outlook for Android<https://aka.ms/ghei36>
________________________________
From: goldenflaw <[email protected]>
Sent: Tuesday, March 13, 2018 6:23:24 PM
To: davidaknowles/leafcutter
Cc: Seyfi, Marilyn; Comment
Subject: Re: [davidaknowles/leafcutter] small sample size affecting cluster significance detection? (#56)
Could you provide the correct mapping of samples to conditions? And your
strongest "hit" from rMATS and or MISO.
Best,
Yang
On Tue, Mar 13, 2018 at 5:21 PM, mh406910 ***@***.***> wrote:
Also when I run your program with the replicates unmerged as separate
replicates I get the same error that there are no significant clusters.
MISO and rMATS both report otherwise.
Get Outlook for Android<https://aka.ms/ghei36>
________________________________
From: goldenflaw ***@***.***>
Sent: Tuesday, March 13, 2018 3:02:47 PM
To: davidaknowles/leafcutter
Cc: Seyfi, Marilyn; Comment
Subject: Re: [davidaknowles/leafcutter] small sample size affecting
cluster significance detection? (#56)
Your P14WTmut.txt file looks wrong, you only have 2 samples in there.
Best,
Yang
On Fri, Mar 9, 2018 at 9:07 AM, Yang Li ***@***.***> wrote:
> I will have a look at the whole thing.
>
> Best,
> Yang
>
> On Mar 9, 2018 8:54 AM, "seyfim" ***@***.***> wrote:
>
>> how do I just share one chromosome with you?
>>
>> —
>> You are receiving this because you were mentioned.
>> Reply to this email directly, view it on GitHub
>> <#56 (comment)-
371835036>,
>> or mute the thread
>> <https://github.com/notifications/unsubscribe-auth/
AE1piZqBGBpzf2cNNshOQCmtkfMdzzChks5tcpe2gaJpZM4Si2YZ>
>> .
>>
>
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub<https://github.com/
davidaknowles/leafcutter#56#issuecomment-372781944>, or mute the
thread<https://github.com/notifications/unsubscribe-auth/
AH0qV7HiNDq4nRYq6MBi9a1xWDnMNfEUks5teBfWgaJpZM4Si2YZ>.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#56 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AE1pif2tfb_R056uBWbmrOrB1zLXuxdoks5teEZOgaJpZM4Si2YZ>
.
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub<#56 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AH0qV4a50BHXeGYRRfHWzlaqB1rvfmN4ks5teEbcgaJpZM4Si2YZ>.
from leafcutter.
mh406910
commented on September 19, 2024
*BAM file
Get Outlook for Android<https://aka.ms/ghei36>
________________________________
From: goldenflaw <[email protected]>
Sent: Tuesday, March 13, 2018 6:23:24 PM
To: davidaknowles/leafcutter
Cc: Seyfi, Marilyn; Comment
Subject: Re: [davidaknowles/leafcutter] small sample size affecting cluster significance detection? (#56)
Could you provide the correct mapping of samples to conditions? And your
strongest "hit" from rMATS and or MISO.
Best,
Yang
On Tue, Mar 13, 2018 at 5:21 PM, mh406910 ***@***.***> wrote:
Also when I run your program with the replicates unmerged as separate
replicates I get the same error that there are no significant clusters.
MISO and rMATS both report otherwise.
Get Outlook for Android<https://aka.ms/ghei36>
________________________________
From: goldenflaw ***@***.***>
Sent: Tuesday, March 13, 2018 3:02:47 PM
To: davidaknowles/leafcutter
Cc: Seyfi, Marilyn; Comment
Subject: Re: [davidaknowles/leafcutter] small sample size affecting
cluster significance detection? (#56)
Your P14WTmut.txt file looks wrong, you only have 2 samples in there.
Best,
Yang
On Fri, Mar 9, 2018 at 9:07 AM, Yang Li ***@***.***> wrote:
> I will have a look at the whole thing.
>
> Best,
> Yang
>
> On Mar 9, 2018 8:54 AM, "seyfim" ***@***.***> wrote:
>
>> how do I just share one chromosome with you?
>>
>> —
>> You are receiving this because you were mentioned.
>> Reply to this email directly, view it on GitHub
>> <#56 (comment)-
371835036>,
>> or mute the thread
>> <https://github.com/notifications/unsubscribe-auth/
AE1piZqBGBpzf2cNNshOQCmtkfMdzzChks5tcpe2gaJpZM4Si2YZ>
>> .
>>
>
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub<https://github.com/
davidaknowles/leafcutter#56#issuecomment-372781944>, or mute the
thread<https://github.com/notifications/unsubscribe-auth/
AH0qV7HiNDq4nRYq6MBi9a1xWDnMNfEUks5teBfWgaJpZM4Si2YZ>.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#56 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AE1pif2tfb_R056uBWbmrOrB1zLXuxdoks5teEZOgaJpZM4Si2YZ>
.
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub<#56 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AH0qV4a50BHXeGYRRfHWzlaqB1rvfmN4ks5teEbcgaJpZM4Si2YZ>.
from leafcutter.
goldenflaw
commented on September 19, 2024
I see that you have 6 samples:
P40M3M4Wt_merged.sorted.filtered.bam P14M3M4Mut_merged.sorted.filtered.bam
P40M3M4Mut_merged.sorted.filtered.bam P14M3M4Wt_merged.sorted.filtered.bam
P40M3M4Het_merged.sorted.filtered.bam P14M3M4Het_merged.sorted.filtered.bam
Could you tell me which ones are "condition 1" and which ones are
"condition 2".
…On Tue, Mar 13, 2018 at 5:25 PM, mh406910 ***@***.***> wrote:
Just to clarify you mean the ban file? As well as the output from rMATS
and MISO with their highest delta pi value for the selected sample
comparison?
Get Outlook for Android<https://aka.ms/ghei36>
________________________________
From: goldenflaw ***@***.***>
Sent: Tuesday, March 13, 2018 6:23:24 PM
To: davidaknowles/leafcutter
Cc: Seyfi, Marilyn; Comment
Subject: Re: [davidaknowles/leafcutter] small sample size affecting
cluster significance detection? (#56)
Could you provide the correct mapping of samples to conditions? And your
strongest "hit" from rMATS and or MISO.
Best,
Yang
On Tue, Mar 13, 2018 at 5:21 PM, mh406910 ***@***.***>
wrote:
> Also when I run your program with the replicates unmerged as separate
> replicates I get the same error that there are no significant clusters.
> MISO and rMATS both report otherwise.
>
> Get Outlook for Android<https://aka.ms/ghei36>
>
> ________________________________
> From: goldenflaw ***@***.***>
> Sent: Tuesday, March 13, 2018 3:02:47 PM
> To: davidaknowles/leafcutter
> Cc: Seyfi, Marilyn; Comment
> Subject: Re: [davidaknowles/leafcutter] small sample size affecting
> cluster significance detection? (#56)
>
> Your P14WTmut.txt file looks wrong, you only have 2 samples in there.
>
> Best,
> Yang
>
> On Fri, Mar 9, 2018 at 9:07 AM, Yang Li ***@***.***> wrote:
>
> > I will have a look at the whole thing.
> >
> > Best,
> > Yang
> >
> > On Mar 9, 2018 8:54 AM, "seyfim" ***@***.***> wrote:
> >
> >> how do I just share one chromosome with you?
> >>
> >> —
> >> You are receiving this because you were mentioned.
> >> Reply to this email directly, view it on GitHub
> >> <#56 (comment)-
> 371835036>,
> >> or mute the thread
> >> <https://github.com/notifications/unsubscribe-auth/
> AE1piZqBGBpzf2cNNshOQCmtkfMdzzChks5tcpe2gaJpZM4Si2YZ>
> >> .
> >>
> >
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub<https://github.com/
> davidaknowles/leafcutter#56#issuecomment-372781944>, or mute the
> thread<https://github.com/notifications/unsubscribe-auth/
> AH0qV7HiNDq4nRYq6MBi9a1xWDnMNfEUks5teBfWgaJpZM4Si2YZ>.
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <#56 (comment)-
372838727>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AE1pif2tfb_
R056uBWbmrOrB1zLXuxdoks5teEZOgaJpZM4Si2YZ>
> .
>
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub<https://github.com/
davidaknowles/leafcutter#56#issuecomment-372839266>, or mute the
thread<https://github.com/notifications/unsubscribe-auth/
AH0qV4a50BHXeGYRRfHWzlaqB1rvfmN4ks5teEbcgaJpZM4Si2YZ>.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#56 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AE1piXefiUjlA0HwvzOEvT5OynDQUxMiks5teEdOgaJpZM4Si2YZ>
.
from leafcutter.
mh406910
commented on September 19, 2024
Well those are not correct.. It should be P14Wt or P40Wt (sample 1) vs P14Mut or P40Mut (sample 2)... I included all comparisons in the .junc step and the following intro cluster step --was that incorrect?
Get Outlook for Android<https://aka.ms/ghei36>
________________________________
From: goldenflaw <[email protected]>
Sent: Tuesday, March 13, 2018 6:27:23 PM
To: davidaknowles/leafcutter
Cc: Seyfi, Marilyn; Comment
Subject: Re: [davidaknowles/leafcutter] small sample size affecting cluster significance detection? (#56)
I see that you have 6 samples:
P40M3M4Wt_merged.sorted.filtered.bam P14M3M4Mut_merged.sorted.filtered.bam
P40M3M4Mut_merged.sorted.filtered.bam P14M3M4Wt_merged.sorted.filtered.bam
P40M3M4Het_merged.sorted.filtered.bam P14M3M4Het_merged.sorted.filtered.bam
Could you tell me which ones are "condition 1" and which ones are
"condition 2".
On Tue, Mar 13, 2018 at 5:25 PM, mh406910 ***@***.***> wrote:
Just to clarify you mean the ban file? As well as the output from rMATS
and MISO with their highest delta pi value for the selected sample
comparison?
Get Outlook for Android<https://aka.ms/ghei36>
________________________________
From: goldenflaw ***@***.***>
Sent: Tuesday, March 13, 2018 6:23:24 PM
To: davidaknowles/leafcutter
Cc: Seyfi, Marilyn; Comment
Subject: Re: [davidaknowles/leafcutter] small sample size affecting
cluster significance detection? (#56)
Could you provide the correct mapping of samples to conditions? And your
strongest "hit" from rMATS and or MISO.
Best,
Yang
On Tue, Mar 13, 2018 at 5:21 PM, mh406910 ***@***.***>
wrote:
> Also when I run your program with the replicates unmerged as separate
> replicates I get the same error that there are no significant clusters.
> MISO and rMATS both report otherwise.
>
> Get Outlook for Android<https://aka.ms/ghei36>
>
> ________________________________
> From: goldenflaw ***@***.***>
> Sent: Tuesday, March 13, 2018 3:02:47 PM
> To: davidaknowles/leafcutter
> Cc: Seyfi, Marilyn; Comment
> Subject: Re: [davidaknowles/leafcutter] small sample size affecting
> cluster significance detection? (#56)
>
> Your P14WTmut.txt file looks wrong, you only have 2 samples in there.
>
> Best,
> Yang
>
> On Fri, Mar 9, 2018 at 9:07 AM, Yang Li ***@***.***> wrote:
>
> > I will have a look at the whole thing.
> >
> > Best,
> > Yang
> >
> > On Mar 9, 2018 8:54 AM, "seyfim" ***@***.***> wrote:
> >
> >> how do I just share one chromosome with you?
> >>
> >> —
> >> You are receiving this because you were mentioned.
> >> Reply to this email directly, view it on GitHub
> >> <#56 (comment)-
> 371835036>,
> >> or mute the thread
> >> <https://github.com/notifications/unsubscribe-auth/
> AE1piZqBGBpzf2cNNshOQCmtkfMdzzChks5tcpe2gaJpZM4Si2YZ>
> >> .
> >>
> >
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub<https://github.com/
> davidaknowles/leafcutter#56#issuecomment-372781944>, or mute the
> thread<https://github.com/notifications/unsubscribe-auth/
> AH0qV7HiNDq4nRYq6MBi9a1xWDnMNfEUks5teBfWgaJpZM4Si2YZ>.
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <#56 (comment)-
372838727>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AE1pif2tfb_
R056uBWbmrOrB1zLXuxdoks5teEZOgaJpZM4Si2YZ>
> .
>
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub<https://github.com/
davidaknowles/leafcutter#56#issuecomment-372839266>, or mute the
thread<https://github.com/notifications/unsubscribe-auth/
AH0qV4a50BHXeGYRRfHWzlaqB1rvfmN4ks5teEbcgaJpZM4Si2YZ>.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#56 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AE1piXefiUjlA0HwvzOEvT5OynDQUxMiks5teEdOgaJpZM4Si2YZ>
.
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub<#56 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AH0qV7Aqc_xXMWmaRAqFAffdAH88FYvWks5teEfKgaJpZM4Si2YZ>.
from leafcutter.
goldenflaw
commented on September 19, 2024
These samples are from the leafcutter output that you gave me (
test_perind_numers.counts.gz
<https://github.com/davidaknowles/leafcutter/files/1797264/test_perind_numers.counts.gz>
)
…On Tue, Mar 13, 2018 at 5:32 PM, mh406910 ***@***.***> wrote:
Well those are not correct.. It should be P14Wt or P40Wt (sample 1) vs
P14Mut or P40Mut (sample 2)... I included all comparisons in the .junc step
and the following intro cluster step --was that incorrect?
Get Outlook for Android<https://aka.ms/ghei36>
________________________________
From: goldenflaw ***@***.***>
Sent: Tuesday, March 13, 2018 6:27:23 PM
To: davidaknowles/leafcutter
Cc: Seyfi, Marilyn; Comment
Subject: Re: [davidaknowles/leafcutter] small sample size affecting
cluster significance detection? (#56)
I see that you have 6 samples:
P40M3M4Wt_merged.sorted.filtered.bam P14M3M4Mut_merged.sorted.filtered.bam
P40M3M4Mut_merged.sorted.filtered.bam P14M3M4Wt_merged.sorted.filtered.bam
P40M3M4Het_merged.sorted.filtered.bam P14M3M4Het_merged.sorted.
filtered.bam
Could you tell me which ones are "condition 1" and which ones are
"condition 2".
On Tue, Mar 13, 2018 at 5:25 PM, mh406910 ***@***.***>
wrote:
> Just to clarify you mean the ban file? As well as the output from rMATS
> and MISO with their highest delta pi value for the selected sample
> comparison?
>
> Get Outlook for Android<https://aka.ms/ghei36>
>
> ________________________________
> From: goldenflaw ***@***.***>
> Sent: Tuesday, March 13, 2018 6:23:24 PM
>
> To: davidaknowles/leafcutter
> Cc: Seyfi, Marilyn; Comment
> Subject: Re: [davidaknowles/leafcutter] small sample size affecting
> cluster significance detection? (#56)
>
> Could you provide the correct mapping of samples to conditions? And your
> strongest "hit" from rMATS and or MISO.
>
> Best,
> Yang
>
> On Tue, Mar 13, 2018 at 5:21 PM, mh406910 ***@***.***>
> wrote:
>
> > Also when I run your program with the replicates unmerged as separate
> > replicates I get the same error that there are no significant clusters.
> > MISO and rMATS both report otherwise.
> >
> > Get Outlook for Android<https://aka.ms/ghei36>
> >
> > ________________________________
> > From: goldenflaw ***@***.***>
> > Sent: Tuesday, March 13, 2018 3:02:47 PM
> > To: davidaknowles/leafcutter
> > Cc: Seyfi, Marilyn; Comment
> > Subject: Re: [davidaknowles/leafcutter] small sample size affecting
> > cluster significance detection? (#56)
> >
> > Your P14WTmut.txt file looks wrong, you only have 2 samples in there.
> >
> > Best,
> > Yang
> >
> > On Fri, Mar 9, 2018 at 9:07 AM, Yang Li ***@***.***> wrote:
> >
> > > I will have a look at the whole thing.
> > >
> > > Best,
> > > Yang
> > >
> > > On Mar 9, 2018 8:54 AM, "seyfim" ***@***.***> wrote:
> > >
> > >> how do I just share one chromosome with you?
> > >>
> > >> —
> > >> You are receiving this because you were mentioned.
> > >> Reply to this email directly, view it on GitHub
> > >> <https://github.com/davidaknowles/leafcutter/
issues/56#issuecomment-
> > 371835036>,
> > >> or mute the thread
> > >> <https://github.com/notifications/unsubscribe-auth/
> > AE1piZqBGBpzf2cNNshOQCmtkfMdzzChks5tcpe2gaJpZM4Si2YZ>
> > >> .
> > >>
> > >
> >
> > —
> > You are receiving this because you commented.
> > Reply to this email directly, view it on GitHub<https://github.com/
> > davidaknowles/leafcutter#56#issuecomment-372781944>, or mute
the
> > thread<https://github.com/notifications/unsubscribe-auth/
> > AH0qV7HiNDq4nRYq6MBi9a1xWDnMNfEUks5teBfWgaJpZM4Si2YZ>.
> >
> > —
> > You are receiving this because you were mentioned.
> > Reply to this email directly, view it on GitHub
> > <#56 (comment)-
> 372838727>,
> > or mute the thread
> > <https://github.com/notifications/unsubscribe-auth/AE1pif2tfb_
> R056uBWbmrOrB1zLXuxdoks5teEZOgaJpZM4Si2YZ>
> > .
> >
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub<https://github.com/
> davidaknowles/leafcutter#56#issuecomment-372839266>, or mute the
> thread<https://github.com/notifications/unsubscribe-auth/
> AH0qV4a50BHXeGYRRfHWzlaqB1rvfmN4ks5teEbcgaJpZM4Si2YZ>.
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <#56 (comment)-
372839683>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/
AE1piXefiUjlA0HwvzOEvT5OynDQUxMiks5teEdOgaJpZM4Si2YZ>
> .
>
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub<https://github.com/
davidaknowles/leafcutter#56#issuecomment-372840184>, or mute the
thread<https://github.com/notifications/unsubscribe-auth/AH0qV7Aqc_
xXMWmaRAqFAffdAH88FYvWks5teEfKgaJpZM4Si2YZ>.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#56 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AE1pifjojIveXOgnlLQb8BSregse9Dcvks5teEkNgaJpZM4Si2YZ>
.
from leafcutter.
mh406910
commented on September 19, 2024
Interesting, well let me rerun,this step it appears something went wrong... Thank you so much for all of your help and when I get back to my office tomorrow morning I will retry step 2 and the following steps! Thank you for taking the time to parse through my data and help me!!! ??
Get Outlook for Android<https://aka.ms/ghei36>
________________________________
From: goldenflaw <[email protected]>
Sent: Tuesday, March 13, 2018 6:35:22 PM
To: davidaknowles/leafcutter
Cc: Seyfi, Marilyn; Comment
Subject: Re: [davidaknowles/leafcutter] small sample size affecting cluster significance detection? (#56)
These samples are from the leafcutter output that you gave me (
test_perind_numers.counts.gz
<https://github.com/davidaknowles/leafcutter/files/1797264/test_perind_numers.counts.gz>
)
On Tue, Mar 13, 2018 at 5:32 PM, mh406910 ***@***.***> wrote:
Well those are not correct.. It should be P14Wt or P40Wt (sample 1) vs
P14Mut or P40Mut (sample 2)... I included all comparisons in the .junc step
and the following intro cluster step --was that incorrect?
Get Outlook for Android<https://aka.ms/ghei36>
________________________________
From: goldenflaw ***@***.***>
Sent: Tuesday, March 13, 2018 6:27:23 PM
To: davidaknowles/leafcutter
Cc: Seyfi, Marilyn; Comment
Subject: Re: [davidaknowles/leafcutter] small sample size affecting
cluster significance detection? (#56)
I see that you have 6 samples:
P40M3M4Wt_merged.sorted.filtered.bam P14M3M4Mut_merged.sorted.filtered.bam
P40M3M4Mut_merged.sorted.filtered.bam P14M3M4Wt_merged.sorted.filtered.bam
P40M3M4Het_merged.sorted.filtered.bam P14M3M4Het_merged.sorted.
filtered.bam
Could you tell me which ones are "condition 1" and which ones are
"condition 2".
On Tue, Mar 13, 2018 at 5:25 PM, mh406910 ***@***.***>
wrote:
> Just to clarify you mean the ban file? As well as the output from rMATS
> and MISO with their highest delta pi value for the selected sample
> comparison?
>
> Get Outlook for Android<https://aka.ms/ghei36>
>
> ________________________________
> From: goldenflaw ***@***.***>
> Sent: Tuesday, March 13, 2018 6:23:24 PM
>
> To: davidaknowles/leafcutter
> Cc: Seyfi, Marilyn; Comment
> Subject: Re: [davidaknowles/leafcutter] small sample size affecting
> cluster significance detection? (#56)
>
> Could you provide the correct mapping of samples to conditions? And your
> strongest "hit" from rMATS and or MISO.
>
> Best,
> Yang
>
> On Tue, Mar 13, 2018 at 5:21 PM, mh406910 ***@***.***>
> wrote:
>
> > Also when I run your program with the replicates unmerged as separate
> > replicates I get the same error that there are no significant clusters.
> > MISO and rMATS both report otherwise.
> >
> > Get Outlook for Android<https://aka.ms/ghei36>
> >
> > ________________________________
> > From: goldenflaw ***@***.***>
> > Sent: Tuesday, March 13, 2018 3:02:47 PM
> > To: davidaknowles/leafcutter
> > Cc: Seyfi, Marilyn; Comment
> > Subject: Re: [davidaknowles/leafcutter] small sample size affecting
> > cluster significance detection? (#56)
> >
> > Your P14WTmut.txt file looks wrong, you only have 2 samples in there.
> >
> > Best,
> > Yang
> >
> > On Fri, Mar 9, 2018 at 9:07 AM, Yang Li ***@***.***> wrote:
> >
> > > I will have a look at the whole thing.
> > >
> > > Best,
> > > Yang
> > >
> > > On Mar 9, 2018 8:54 AM, "seyfim" ***@***.***> wrote:
> > >
> > >> how do I just share one chromosome with you?
> > >>
> > >> —
> > >> You are receiving this because you were mentioned.
> > >> Reply to this email directly, view it on GitHub
> > >> <https://github.com/davidaknowles/leafcutter/
issues/56#issuecomment-
> > 371835036>,
> > >> or mute the thread
> > >> <https://github.com/notifications/unsubscribe-auth/
> > AE1piZqBGBpzf2cNNshOQCmtkfMdzzChks5tcpe2gaJpZM4Si2YZ>
> > >> .
> > >>
> > >
> >
> > —
> > You are receiving this because you commented.
> > Reply to this email directly, view it on GitHub<https://github.com/
> > davidaknowles/leafcutter#56#issuecomment-372781944>, or mute
the
> > thread<https://github.com/notifications/unsubscribe-auth/
> > AH0qV7HiNDq4nRYq6MBi9a1xWDnMNfEUks5teBfWgaJpZM4Si2YZ>.
> >
> > —
> > You are receiving this because you were mentioned.
> > Reply to this email directly, view it on GitHub
> > <#56 (comment)-
> 372838727>,
> > or mute the thread
> > <https://github.com/notifications/unsubscribe-auth/AE1pif2tfb_
> R056uBWbmrOrB1zLXuxdoks5teEZOgaJpZM4Si2YZ>
> > .
> >
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub<https://github.com/
> davidaknowles/leafcutter#56#issuecomment-372839266>, or mute the
> thread<https://github.com/notifications/unsubscribe-auth/
> AH0qV4a50BHXeGYRRfHWzlaqB1rvfmN4ks5teEbcgaJpZM4Si2YZ>.
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <#56 (comment)-
372839683>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/
AE1piXefiUjlA0HwvzOEvT5OynDQUxMiks5teEdOgaJpZM4Si2YZ>
> .
>
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub<https://github.com/
davidaknowles/leafcutter#56#issuecomment-372840184>, or mute the
thread<https://github.com/notifications/unsubscribe-auth/AH0qV7Aqc_
xXMWmaRAqFAffdAH88FYvWks5teEfKgaJpZM4Si2YZ>.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#56 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AE1pifjojIveXOgnlLQb8BSregse9Dcvks5teEkNgaJpZM4Si2YZ>
.
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub<#56 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AH0qVyVeY6qZqaqwDsXLAfyjgplfknB6ks5teEmqgaJpZM4Si2YZ>.
from leafcutter.
mh406910
commented on September 19, 2024
Hello,
So after reviewing the files I did have the correct samples. The comparisons are as follows:
P14M3M4Wt_merged.sorted.filtered.bam vs P14M3M4Mut_merged.sorted.filtered.bam
P14M3M4Wt_merged.sorted.filtered.bam vs P14M3M4Het_merged.sorted.filtered.bam
P14M3M4Mut_merged.sorted.filtered.bam . vs P14M3M4Het_merged.sorted.filtered.bam
P40M3M4Wt_merged.sorted.filtered.bam vs P40M3M4Mut_merged.sorted.filtered.bam
P40M3M4Wt_merged.sorted.filtered.bam vs P40M3M4Het_merged.sorted.filtered.bam
P40M3M4Mut_merged.sorted.filtered.bam vs P40M3M4Het_merged.sorted.filtered.bam
Thanks,
Marilyn E. Seyfi
Bioinformatics Technologist
Cleveland Clinic Genomic Medicine Institute
work email: [email protected]
mobile: (740)-603-2131
________________________________
From: goldenflaw <[email protected]>
Sent: Tuesday, March 13, 2018 6:35 PM
To: davidaknowles/leafcutter
Cc: Seyfi, Marilyn; Comment
Subject: Re: [davidaknowles/leafcutter] small sample size affecting cluster significance detection? (#56)
These samples are from the leafcutter output that you gave me (
test_perind_numers.counts.gz
<https://github.com/davidaknowles/leafcutter/files/1797264/test_perind_numers.counts.gz>
)
On Tue, Mar 13, 2018 at 5:32 PM, mh406910 ***@***.***> wrote:
Well those are not correct.. It should be P14Wt or P40Wt (sample 1) vs
P14Mut or P40Mut (sample 2)... I included all comparisons in the .junc step
and the following intro cluster step --was that incorrect?
Get Outlook for Android<https://aka.ms/ghei36>
________________________________
From: goldenflaw ***@***.***>
Sent: Tuesday, March 13, 2018 6:27:23 PM
To: davidaknowles/leafcutter
Cc: Seyfi, Marilyn; Comment
Subject: Re: [davidaknowles/leafcutter] small sample size affecting
cluster significance detection? (#56)
I see that you have 6 samples:
P40M3M4Wt_merged.sorted.filtered.bam P14M3M4Mut_merged.sorted.filtered.bam
P40M3M4Mut_merged.sorted.filtered.bam P14M3M4Wt_merged.sorted.filtered.bam
P40M3M4Het_merged.sorted.filtered.bam P14M3M4Het_merged.sorted.
filtered.bam
Could you tell me which ones are "condition 1" and which ones are
"condition 2".
On Tue, Mar 13, 2018 at 5:25 PM, mh406910 ***@***.***>
wrote:
> Just to clarify you mean the ban file? As well as the output from rMATS
> and MISO with their highest delta pi value for the selected sample
> comparison?
>
> Get Outlook for Android<https://aka.ms/ghei36>
>
> ________________________________
> From: goldenflaw ***@***.***>
> Sent: Tuesday, March 13, 2018 6:23:24 PM
>
> To: davidaknowles/leafcutter
> Cc: Seyfi, Marilyn; Comment
> Subject: Re: [davidaknowles/leafcutter] small sample size affecting
> cluster significance detection? (#56)
>
> Could you provide the correct mapping of samples to conditions? And your
> strongest "hit" from rMATS and or MISO.
>
> Best,
> Yang
>
> On Tue, Mar 13, 2018 at 5:21 PM, mh406910 ***@***.***>
> wrote:
>
> > Also when I run your program with the replicates unmerged as separate
> > replicates I get the same error that there are no significant clusters.
> > MISO and rMATS both report otherwise.
> >
> > Get Outlook for Android<https://aka.ms/ghei36>
> >
> > ________________________________
> > From: goldenflaw ***@***.***>
> > Sent: Tuesday, March 13, 2018 3:02:47 PM
> > To: davidaknowles/leafcutter
> > Cc: Seyfi, Marilyn; Comment
> > Subject: Re: [davidaknowles/leafcutter] small sample size affecting
> > cluster significance detection? (#56)
> >
> > Your P14WTmut.txt file looks wrong, you only have 2 samples in there.
> >
> > Best,
> > Yang
> >
> > On Fri, Mar 9, 2018 at 9:07 AM, Yang Li ***@***.***> wrote:
> >
> > > I will have a look at the whole thing.
> > >
> > > Best,
> > > Yang
> > >
> > > On Mar 9, 2018 8:54 AM, "seyfim" ***@***.***> wrote:
> > >
> > >> how do I just share one chromosome with you?
> > >>
> > >> —
> > >> You are receiving this because you were mentioned.
> > >> Reply to this email directly, view it on GitHub
> > >> <https://github.com/davidaknowles/leafcutter/
issues/56#issuecomment-
> > 371835036>,
> > >> or mute the thread
> > >> <https://github.com/notifications/unsubscribe-auth/
> > AE1piZqBGBpzf2cNNshOQCmtkfMdzzChks5tcpe2gaJpZM4Si2YZ>
> > >> .
> > >>
> > >
> >
> > —
> > You are receiving this because you commented.
> > Reply to this email directly, view it on GitHub<https://github.com/
> > davidaknowles/leafcutter#56#issuecomment-372781944>, or mute
the
> > thread<https://github.com/notifications/unsubscribe-auth/
> > AH0qV7HiNDq4nRYq6MBi9a1xWDnMNfEUks5teBfWgaJpZM4Si2YZ>.
> >
> > —
> > You are receiving this because you were mentioned.
> > Reply to this email directly, view it on GitHub
> > <#56 (comment)-
> 372838727>,
> > or mute the thread
> > <https://github.com/notifications/unsubscribe-auth/AE1pif2tfb_
> R056uBWbmrOrB1zLXuxdoks5teEZOgaJpZM4Si2YZ>
> > .
> >
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub<https://github.com/
> davidaknowles/leafcutter#56#issuecomment-372839266>, or mute the
> thread<https://github.com/notifications/unsubscribe-auth/
> AH0qV4a50BHXeGYRRfHWzlaqB1rvfmN4ks5teEbcgaJpZM4Si2YZ>.
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <#56 (comment)-
372839683>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/
AE1piXefiUjlA0HwvzOEvT5OynDQUxMiks5teEdOgaJpZM4Si2YZ>
> .
>
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub<https://github.com/
davidaknowles/leafcutter#56#issuecomment-372840184>, or mute the
thread<https://github.com/notifications/unsubscribe-auth/AH0qV7Aqc_
xXMWmaRAqFAffdAH88FYvWks5teEfKgaJpZM4Si2YZ>.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#56 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AE1pifjojIveXOgnlLQb8BSregse9Dcvks5teEkNgaJpZM4Si2YZ>
.
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub<#56 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AH0qVyVeY6qZqaqwDsXLAfyjgplfknB6ks5teEmqgaJpZM4Si2YZ>.
from leafcutter.
goldenflaw
commented on September 19, 2024
Thanks, but I'm not sure I understand? Which 3 samples are condition 1 and
which 3 are condition 2?
Best,
Yang
…On Wed, Mar 14, 2018 at 11:21 AM, mh406910 ***@***.***> wrote:
Hello,
So after reviewing the files I did have the correct samples. The
comparisons are as follows:
P14M3M4Wt_merged.sorted.filtered.bam vs P14M3M4Mut_merged.sorted.
filtered.bam
P14M3M4Wt_merged.sorted.filtered.bam vs P14M3M4Het_merged.sorted.
filtered.bam
P14M3M4Mut_merged.sorted.filtered.bam . vs P14M3M4Het_merged.sorted.
filtered.bam
P40M3M4Wt_merged.sorted.filtered.bam vs P40M3M4Mut_merged.sorted.
filtered.bam
P40M3M4Wt_merged.sorted.filtered.bam vs P40M3M4Het_merged.sorted.
filtered.bam
P40M3M4Mut_merged.sorted.filtered.bam vs P40M3M4Het_merged.sorted.
filtered.bam
Thanks,
Marilyn E. Seyfi
Bioinformatics Technologist
Cleveland Clinic Genomic Medicine Institute
work email: ***@***.***
mobile: (740)-603-2131 <(740)%20603-2131>
________________________________
From: goldenflaw ***@***.***>
Sent: Tuesday, March 13, 2018 6:35 PM
To: davidaknowles/leafcutter
Cc: Seyfi, Marilyn; Comment
Subject: Re: [davidaknowles/leafcutter] small sample size affecting
cluster significance detection? (#56)
These samples are from the leafcutter output that you gave me (
test_perind_numers.counts.gz
<https://github.com/davidaknowles/leafcutter/files/1797264/test_perind_
numers.counts.gz>
)
On Tue, Mar 13, 2018 at 5:32 PM, mh406910 ***@***.***>
wrote:
> Well those are not correct.. It should be P14Wt or P40Wt (sample 1) vs
> P14Mut or P40Mut (sample 2)... I included all comparisons in the .junc
step
> and the following intro cluster step --was that incorrect?
>
> Get Outlook for Android<https://aka.ms/ghei36>
>
> ________________________________
> From: goldenflaw ***@***.***>
> Sent: Tuesday, March 13, 2018 6:27:23 PM
>
> To: davidaknowles/leafcutter
> Cc: Seyfi, Marilyn; Comment
> Subject: Re: [davidaknowles/leafcutter] small sample size affecting
> cluster significance detection? (#56)
>
> I see that you have 6 samples:
>
> P40M3M4Wt_merged.sorted.filtered.bam P14M3M4Mut_merged.sorted.
filtered.bam
> P40M3M4Mut_merged.sorted.filtered.bam P14M3M4Wt_merged.sorted.
filtered.bam
> P40M3M4Het_merged.sorted.filtered.bam P14M3M4Het_merged.sorted.
> filtered.bam
>
>
> Could you tell me which ones are "condition 1" and which ones are
> "condition 2".
>
> On Tue, Mar 13, 2018 at 5:25 PM, mh406910 ***@***.***>
> wrote:
>
> > Just to clarify you mean the ban file? As well as the output from rMATS
> > and MISO with their highest delta pi value for the selected sample
> > comparison?
> >
> > Get Outlook for Android<https://aka.ms/ghei36>
> >
> > ________________________________
> > From: goldenflaw ***@***.***>
> > Sent: Tuesday, March 13, 2018 6:23:24 PM
> >
> > To: davidaknowles/leafcutter
> > Cc: Seyfi, Marilyn; Comment
> > Subject: Re: [davidaknowles/leafcutter] small sample size affecting
> > cluster significance detection? (#56)
> >
> > Could you provide the correct mapping of samples to conditions? And
your
> > strongest "hit" from rMATS and or MISO.
> >
> > Best,
> > Yang
> >
> > On Tue, Mar 13, 2018 at 5:21 PM, mh406910 ***@***.***>
> > wrote:
> >
> > > Also when I run your program with the replicates unmerged as separate
> > > replicates I get the same error that there are no significant
clusters.
> > > MISO and rMATS both report otherwise.
> > >
> > > Get Outlook for Android<https://aka.ms/ghei36>
> > >
> > > ________________________________
> > > From: goldenflaw ***@***.***>
> > > Sent: Tuesday, March 13, 2018 3:02:47 PM
> > > To: davidaknowles/leafcutter
> > > Cc: Seyfi, Marilyn; Comment
> > > Subject: Re: [davidaknowles/leafcutter] small sample size affecting
> > > cluster significance detection? (#56)
> > >
> > > Your P14WTmut.txt file looks wrong, you only have 2 samples in there.
> > >
> > > Best,
> > > Yang
> > >
> > > On Fri, Mar 9, 2018 at 9:07 AM, Yang Li ***@***.***>
wrote:
> > >
> > > > I will have a look at the whole thing.
> > > >
> > > > Best,
> > > > Yang
> > > >
> > > > On Mar 9, 2018 8:54 AM, "seyfim" ***@***.***> wrote:
> > > >
> > > >> how do I just share one chromosome with you?
> > > >>
> > > >> —
> > > >> You are receiving this because you were mentioned.
> > > >> Reply to this email directly, view it on GitHub
> > > >> <https://github.com/davidaknowles/leafcutter/
> issues/56#issuecomment-
> > > 371835036>,
> > > >> or mute the thread
> > > >> <https://github.com/notifications/unsubscribe-auth/
> > > AE1piZqBGBpzf2cNNshOQCmtkfMdzzChks5tcpe2gaJpZM4Si2YZ>
> > > >> .
> > > >>
> > > >
> > >
> > > —
> > > You are receiving this because you commented.
> > > Reply to this email directly, view it on GitHub<https://github.com/
> > > davidaknowles/leafcutter#56#issuecomment-372781944>, or mute
> the
> > > thread<https://github.com/notifications/unsubscribe-auth/
> > > AH0qV7HiNDq4nRYq6MBi9a1xWDnMNfEUks5teBfWgaJpZM4Si2YZ>.
> > >
> > > —
> > > You are receiving this because you were mentioned.
> > > Reply to this email directly, view it on GitHub
> > > <#56 (comment)-
> > 372838727>,
> > > or mute the thread
> > > <https://github.com/notifications/unsubscribe-auth/AE1pif2tfb_
> > R056uBWbmrOrB1zLXuxdoks5teEZOgaJpZM4Si2YZ>
> > > .
> > >
> >
> > —
> > You are receiving this because you commented.
> > Reply to this email directly, view it on GitHub<https://github.com/
> > davidaknowles/leafcutter#56#issuecomment-372839266>, or mute
the
> > thread<https://github.com/notifications/unsubscribe-auth/
> > AH0qV4a50BHXeGYRRfHWzlaqB1rvfmN4ks5teEbcgaJpZM4Si2YZ>.
> >
> > —
> > You are receiving this because you were mentioned.
> > Reply to this email directly, view it on GitHub
> > <#56 (comment)-
> 372839683>,
> > or mute the thread
> > <https://github.com/notifications/unsubscribe-auth/
> AE1piXefiUjlA0HwvzOEvT5OynDQUxMiks5teEdOgaJpZM4Si2YZ>
> > .
> >
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub<https://github.com/
> davidaknowles/leafcutter#56#issuecomment-372840184>, or mute the
> thread<https://github.com/notifications/unsubscribe-auth/AH0qV7Aqc_
> xXMWmaRAqFAffdAH88FYvWks5teEfKgaJpZM4Si2YZ>.
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <#56 (comment)-
372841413>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/
AE1pifjojIveXOgnlLQb8BSregse9Dcvks5teEkNgaJpZM4Si2YZ>
> .
>
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub<https://github.com/
davidaknowles/leafcutter#56#issuecomment-372842066>, or mute the
thread<https://github.com/notifications/unsubscribe-auth/
AH0qVyVeY6qZqaqwDsXLAfyjgplfknB6ks5teEmqgaJpZM4Si2YZ>.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#56 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AE1picyeYN0qgm8x_1MbtBCWV5AT8eLNks5teUNwgaJpZM4Si2YZ>
.
from leafcutter.
seyfim
commented on September 19, 2024
I have two sets (either P14M3M4 or P40M3M4) and the comparisons for each set are sample1: Wt, Wt, Mut then sample 2: Mut, Het, Het respectively
On Mar 14, 2018, at 12:33 PM, goldenflaw <[email protected]<mailto:[email protected]>> wrote:
Thanks, but I'm not sure I understand? Which 3 samples are condition 1 and
which 3 are condition 2?
Best,
Yang
On Wed, Mar 14, 2018 at 11:21 AM, mh406910 ***@***.******@***.***>> wrote:
Hello,
So after reviewing the files I did have the correct samples. The
comparisons are as follows:
P14M3M4Wt_merged.sorted.filtered.bam vs P14M3M4Mut_merged.sorted.
filtered.bam
P14M3M4Wt_merged.sorted.filtered.bam vs P14M3M4Het_merged.sorted.
filtered.bam
P14M3M4Mut_merged.sorted.filtered.bam . vs P14M3M4Het_merged.sorted.
filtered.bam
P40M3M4Wt_merged.sorted.filtered.bam vs P40M3M4Mut_merged.sorted.
filtered.bam
P40M3M4Wt_merged.sorted.filtered.bam vs P40M3M4Het_merged.sorted.
filtered.bam
P40M3M4Mut_merged.sorted.filtered.bam vs P40M3M4Het_merged.sorted.
filtered.bam
Thanks,
Marilyn E. Seyfi
Bioinformatics Technologist
Cleveland Clinic Genomic Medicine Institute
work email: ***@***.******@***.***>
mobile: (740)-603-2131 <(740)%20603-2131>
________________________________
From: goldenflaw ***@***.******@***.***>>
Sent: Tuesday, March 13, 2018 6:35 PM
To: davidaknowles/leafcutter
Cc: Seyfi, Marilyn; Comment
Subject: Re: [davidaknowles/leafcutter] small sample size affecting
cluster significance detection? (#56)
These samples are from the leafcutter output that you gave me (
test_perind_numers.counts.gz
<https://github.com/davidaknowles/leafcutter/files/1797264/test_perind_
numers.counts.gz>
)
On Tue, Mar 13, 2018 at 5:32 PM, mh406910 ***@***.******@***.***>>
wrote:
> Well those are not correct.. It should be P14Wt or P40Wt (sample 1) vs
> P14Mut or P40Mut (sample 2)... I included all comparisons in the .junc
step
> and the following intro cluster step --was that incorrect?
>
> Get Outlook for Android<https://aka.ms/ghei36>
>
> ________________________________
> From: goldenflaw ***@***.******@***.***>>
> Sent: Tuesday, March 13, 2018 6:27:23 PM
>
> To: davidaknowles/leafcutter
> Cc: Seyfi, Marilyn; Comment
> Subject: Re: [davidaknowles/leafcutter] small sample size affecting
> cluster significance detection? (#56)
>
> I see that you have 6 samples:
>
> P40M3M4Wt_merged.sorted.filtered.bam P14M3M4Mut_merged.sorted.
filtered.bam
> P40M3M4Mut_merged.sorted.filtered.bam P14M3M4Wt_merged.sorted.
filtered.bam
> P40M3M4Het_merged.sorted.filtered.bam P14M3M4Het_merged.sorted.
> filtered.bam
>
>
> Could you tell me which ones are "condition 1" and which ones are
> "condition 2".
>
> On Tue, Mar 13, 2018 at 5:25 PM, mh406910 ***@***.******@***.***>>
> wrote:
>
> > Just to clarify you mean the ban file? As well as the output from rMATS
> > and MISO with their highest delta pi value for the selected sample
> > comparison?
> >
> > Get Outlook for Android<https://aka.ms/ghei36>
> >
> > ________________________________
> > From: goldenflaw ***@***.******@***.***>>
> > Sent: Tuesday, March 13, 2018 6:23:24 PM
> >
> > To: davidaknowles/leafcutter
> > Cc: Seyfi, Marilyn; Comment
> > Subject: Re: [davidaknowles/leafcutter] small sample size affecting
> > cluster significance detection? (#56)
> >
> > Could you provide the correct mapping of samples to conditions? And
your
> > strongest "hit" from rMATS and or MISO.
> >
> > Best,
> > Yang
> >
> > On Tue, Mar 13, 2018 at 5:21 PM, mh406910 ***@***.******@***.***>>
> > wrote:
> >
> > > Also when I run your program with the replicates unmerged as separate
> > > replicates I get the same error that there are no significant
clusters.
> > > MISO and rMATS both report otherwise.
> > >
> > > Get Outlook for Android<https://aka.ms/ghei36>
> > >
> > > ________________________________
> > > From: goldenflaw ***@***.******@***.***>>
> > > Sent: Tuesday, March 13, 2018 3:02:47 PM
> > > To: davidaknowles/leafcutter
> > > Cc: Seyfi, Marilyn; Comment
> > > Subject: Re: [davidaknowles/leafcutter] small sample size affecting
> > > cluster significance detection? (#56)
> > >
> > > Your P14WTmut.txt file looks wrong, you only have 2 samples in there.
> > >
> > > Best,
> > > Yang
> > >
> > > On Fri, Mar 9, 2018 at 9:07 AM, Yang Li ***@***.******@***.***>>
wrote:
> > >
> > > > I will have a look at the whole thing.
> > > >
> > > > Best,
> > > > Yang
> > > >
> > > > On Mar 9, 2018 8:54 AM, "seyfim" ***@***.******@***.***>> wrote:
> > > >
> > > >> how do I just share one chromosome with you?
> > > >>
> > > >> —
> > > >> You are receiving this because you were mentioned.
> > > >> Reply to this email directly, view it on GitHub
> > > >> <https://github.com/davidaknowles/leafcutter/
> issues/56#issuecomment-
> > > 371835036>,
> > > >> or mute the thread
> > > >> <https://github.com/notifications/unsubscribe-auth/
> > > AE1piZqBGBpzf2cNNshOQCmtkfMdzzChks5tcpe2gaJpZM4Si2YZ>
> > > >> .
> > > >>
> > > >
> > >
> > > —
> > > You are receiving this because you commented.
> > > Reply to this email directly, view it on GitHub<https://github.com/
> > > davidaknowles/leafcutter#56#issuecomment-372781944>, or mute
> the
> > > thread<https://github.com/notifications/unsubscribe-auth/
> > > AH0qV7HiNDq4nRYq6MBi9a1xWDnMNfEUks5teBfWgaJpZM4Si2YZ>.
> > >
> > > —
> > > You are receiving this because you were mentioned.
> > > Reply to this email directly, view it on GitHub
> > > <#56 (comment)-
> > 372838727>,
> > > or mute the thread
> > > <https://github.com/notifications/unsubscribe-auth/AE1pif2tfb_
> > R056uBWbmrOrB1zLXuxdoks5teEZOgaJpZM4Si2YZ>
> > > .
> > >
> >
> > —
> > You are receiving this because you commented.
> > Reply to this email directly, view it on GitHub<https://github.com/
> > davidaknowles/leafcutter#56#issuecomment-372839266>, or mute
the
> > thread<https://github.com/notifications/unsubscribe-auth/
> > AH0qV4a50BHXeGYRRfHWzlaqB1rvfmN4ks5teEbcgaJpZM4Si2YZ>.
> >
> > —
> > You are receiving this because you were mentioned.
> > Reply to this email directly, view it on GitHub
> > <#56 (comment)-
> 372839683>,
> > or mute the thread
> > <https://github.com/notifications/unsubscribe-auth/
> AE1piXefiUjlA0HwvzOEvT5OynDQUxMiks5teEdOgaJpZM4Si2YZ>
> > .
> >
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub<https://github.com/
> davidaknowles/leafcutter#56#issuecomment-372840184>, or mute the
> thread<https://github.com/notifications/unsubscribe-auth/AH0qV7Aqc_
> xXMWmaRAqFAffdAH88FYvWks5teEfKgaJpZM4Si2YZ>.
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <#56 (comment)-
372841413>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/
AE1pifjojIveXOgnlLQb8BSregse9Dcvks5teEkNgaJpZM4Si2YZ>
> .
>
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub<https://github.com/
davidaknowles/leafcutter#56#issuecomment-372842066>, or mute the
thread<https://github.com/notifications/unsubscribe-auth/
AH0qVyVeY6qZqaqwDsXLAfyjgplfknB6ks5teEmqgaJpZM4Si2YZ>.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#56 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AE1picyeYN0qgm8x_1MbtBCWV5AT8eLNks5teUNwgaJpZM4Si2YZ>
.
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub<#56 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AikLJbxBarvHE4PBpQbaL4R-FYiOc51Nks5teUZhgaJpZM4Si2YZ>.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
from leafcutter.
goldenflaw
commented on September 19, 2024
I'm still confused are the assignments as such:
P40M3M4Wt_merged.sorted.filtered.bam 2
P14M3M4Mut_merged.sorted.filtered.bam 1
P40M3M4Mut_merged.sorted.filtered.bam 2
P14M3M4Wt_merged.sorted.filtered.bam 1
P40M3M4Het_merged.sorted.filtered.bam 2
P14M3M4Het_merged.sorted.filtered.bam 1
…On Wed, Mar 14, 2018 at 11:36 AM, seyfim ***@***.***> wrote:
I have two sets (either P14M3M4 or P40M3M4) and the comparisons for each
set are sample1: Wt, Wt, Mut then sample 2: Mut, Het, Het respectively
On Mar 14, 2018, at 12:33 PM, goldenflaw ***@***.***<mailto:
***@***.***>> wrote:
Thanks, but I'm not sure I understand? Which 3 samples are condition 1 and
which 3 are condition 2?
Best,
Yang
On Wed, Mar 14, 2018 at 11:21 AM, mh406910 ***@***.***<
***@***.***>> wrote:
> Hello,
>
> So after reviewing the files I did have the correct samples. The
> comparisons are as follows:
>
>
>
> P14M3M4Wt_merged.sorted.filtered.bam vs P14M3M4Mut_merged.sorted.
> filtered.bam
>
> P14M3M4Wt_merged.sorted.filtered.bam vs P14M3M4Het_merged.sorted.
> filtered.bam
>
> P14M3M4Mut_merged.sorted.filtered.bam . vs P14M3M4Het_merged.sorted.
> filtered.bam
>
> P40M3M4Wt_merged.sorted.filtered.bam vs P40M3M4Mut_merged.sorted.
> filtered.bam
>
> P40M3M4Wt_merged.sorted.filtered.bam vs P40M3M4Het_merged.sorted.
> filtered.bam
>
> P40M3M4Mut_merged.sorted.filtered.bam vs P40M3M4Het_merged.sorted.
> filtered.bam
>
>
> Thanks,
> Marilyn E. Seyfi
> Bioinformatics Technologist
> Cleveland Clinic Genomic Medicine Institute
> work email: ***@***.******@***.***>
> mobile: (740)-603-2131 <(740)%20603-2131> <(740)%20603-2131>
>
>
>
>
> ________________________________
> From: goldenflaw ***@***.******@***.***
com>>
> Sent: Tuesday, March 13, 2018 6:35 PM
>
> To: davidaknowles/leafcutter
> Cc: Seyfi, Marilyn; Comment
> Subject: Re: [davidaknowles/leafcutter] small sample size affecting
> cluster significance detection? (#56)
>
> These samples are from the leafcutter output that you gave me (
> test_perind_numers.counts.gz
> <https://github.com/davidaknowles/leafcutter/files/1797264/test_perind_
> numers.counts.gz>
> )
>
> On Tue, Mar 13, 2018 at 5:32 PM, mh406910 ***@***.***<
***@***.***>>
> wrote:
>
> > Well those are not correct.. It should be P14Wt or P40Wt (sample 1) vs
> > P14Mut or P40Mut (sample 2)... I included all comparisons in the .junc
> step
> > and the following intro cluster step --was that incorrect?
> >
> > Get Outlook for Android<https://aka.ms/ghei36>
> >
> > ________________________________
> > From: goldenflaw ***@***.***<mailto:
***@***.***>>
> > Sent: Tuesday, March 13, 2018 6:27:23 PM
> >
> > To: davidaknowles/leafcutter
> > Cc: Seyfi, Marilyn; Comment
> > Subject: Re: [davidaknowles/leafcutter] small sample size affecting
> > cluster significance detection? (#56)
> >
> > I see that you have 6 samples:
> >
> > P40M3M4Wt_merged.sorted.filtered.bam P14M3M4Mut_merged.sorted.
> filtered.bam
> > P40M3M4Mut_merged.sorted.filtered.bam P14M3M4Wt_merged.sorted.
> filtered.bam
> > P40M3M4Het_merged.sorted.filtered.bam P14M3M4Het_merged.sorted.
> > filtered.bam
> >
> >
> > Could you tell me which ones are "condition 1" and which ones are
> > "condition 2".
> >
> > On Tue, Mar 13, 2018 at 5:25 PM, mh406910 ***@***.***<
***@***.***>>
> > wrote:
> >
> > > Just to clarify you mean the ban file? As well as the output from
rMATS
> > > and MISO with their highest delta pi value for the selected sample
> > > comparison?
> > >
> > > Get Outlook for Android<https://aka.ms/ghei36>
> > >
> > > ________________________________
> > > From: goldenflaw ***@***.***<mailto:
***@***.***>>
> > > Sent: Tuesday, March 13, 2018 6:23:24 PM
> > >
> > > To: davidaknowles/leafcutter
> > > Cc: Seyfi, Marilyn; Comment
> > > Subject: Re: [davidaknowles/leafcutter] small sample size affecting
> > > cluster significance detection? (#56)
> > >
> > > Could you provide the correct mapping of samples to conditions? And
> your
> > > strongest "hit" from rMATS and or MISO.
> > >
> > > Best,
> > > Yang
> > >
> > > On Tue, Mar 13, 2018 at 5:21 PM, mh406910 ***@***.***<
***@***.***>>
> > > wrote:
> > >
> > > > Also when I run your program with the replicates unmerged as
separate
> > > > replicates I get the same error that there are no significant
> clusters.
> > > > MISO and rMATS both report otherwise.
> > > >
> > > > Get Outlook for Android<https://aka.ms/ghei36>
> > > >
> > > > ________________________________
> > > > From: goldenflaw ***@***.***<mailto:
***@***.***>>
> > > > Sent: Tuesday, March 13, 2018 3:02:47 PM
> > > > To: davidaknowles/leafcutter
> > > > Cc: Seyfi, Marilyn; Comment
> > > > Subject: Re: [davidaknowles/leafcutter] small sample size
affecting
> > > > cluster significance detection? (#56)
> > > >
> > > > Your P14WTmut.txt file looks wrong, you only have 2 samples in
there.
> > > >
> > > > Best,
> > > > Yang
> > > >
> > > > On Fri, Mar 9, 2018 at 9:07 AM, Yang Li ***@***.***
***@***.***>>
> wrote:
> > > >
> > > > > I will have a look at the whole thing.
> > > > >
> > > > > Best,
> > > > > Yang
> > > > >
> > > > > On Mar 9, 2018 8:54 AM, "seyfim" ***@***.***<
***@***.***>> wrote:
> > > > >
> > > > >> how do I just share one chromosome with you?
> > > > >>
> > > > >> —
> > > > >> You are receiving this because you were mentioned.
> > > > >> Reply to this email directly, view it on GitHub
> > > > >> <https://github.com/davidaknowles/leafcutter/
> > issues/56#issuecomment-
> > > > 371835036>,
> > > > >> or mute the thread
> > > > >> <https://github.com/notifications/unsubscribe-auth/
> > > > AE1piZqBGBpzf2cNNshOQCmtkfMdzzChks5tcpe2gaJpZM4Si2YZ>
> > > > >> .
> > > > >>
> > > > >
> > > >
> > > > —
> > > > You are receiving this because you commented.
> > > > Reply to this email directly, view it on GitHub<
https://github.com/
> > > > davidaknowles/leafcutter#56#issuecomment-372781944>, or
mute
> > the
> > > > thread<https://github.com/notifications/unsubscribe-auth/
> > > > AH0qV7HiNDq4nRYq6MBi9a1xWDnMNfEUks5teBfWgaJpZM4Si2YZ>.
> > > >
> > > > —
> > > > You are receiving this because you were mentioned.
> > > > Reply to this email directly, view it on GitHub
> > > > <https://github.com/davidaknowles/leafcutter/
issues/56#issuecomment-
> > > 372838727>,
> > > > or mute the thread
> > > > <https://github.com/notifications/unsubscribe-auth/AE1pif2tfb_
> > > R056uBWbmrOrB1zLXuxdoks5teEZOgaJpZM4Si2YZ>
> > > > .
> > > >
> > >
> > > —
> > > You are receiving this because you commented.
> > > Reply to this email directly, view it on GitHub<https://github.com/
> > > davidaknowles/leafcutter#56#issuecomment-372839266>, or mute
> the
> > > thread<https://github.com/notifications/unsubscribe-auth/
> > > AH0qV4a50BHXeGYRRfHWzlaqB1rvfmN4ks5teEbcgaJpZM4Si2YZ>.
> > >
> > > —
> > > You are receiving this because you were mentioned.
> > > Reply to this email directly, view it on GitHub
> > > <#56 (comment)-
> > 372839683>,
> > > or mute the thread
> > > <https://github.com/notifications/unsubscribe-auth/
> > AE1piXefiUjlA0HwvzOEvT5OynDQUxMiks5teEdOgaJpZM4Si2YZ>
> > > .
> > >
> >
> > —
> > You are receiving this because you commented.
> > Reply to this email directly, view it on GitHub<https://github.com/
> > davidaknowles/leafcutter#56#issuecomment-372840184>, or mute
the
> > thread<https://github.com/notifications/unsubscribe-auth/AH0qV7Aqc_
> > xXMWmaRAqFAffdAH88FYvWks5teEfKgaJpZM4Si2YZ>.
> >
> > —
> > You are receiving this because you were mentioned.
> > Reply to this email directly, view it on GitHub
> > <#56 (comment)-
> 372841413>,
> > or mute the thread
> > <https://github.com/notifications/unsubscribe-auth/
> AE1pifjojIveXOgnlLQb8BSregse9Dcvks5teEkNgaJpZM4Si2YZ>
> > .
> >
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub<https://github.com/
> davidaknowles/leafcutter#56#issuecomment-372842066>, or mute the
> thread<https://github.com/notifications/unsubscribe-auth/
> AH0qVyVeY6qZqaqwDsXLAfyjgplfknB6ks5teEmqgaJpZM4Si2YZ>.
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <#56 (comment)-
373083237>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AE1picyeYN0qgm8x_
1MbtBCWV5AT8eLNks5teUNwgaJpZM4Si2YZ>
> .
>
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub<https://github.com/
davidaknowles/leafcutter#56#issuecomment-373087793>, or mute the
thread<https://github.com/notifications/unsubscribe-
auth/AikLJbxBarvHE4PBpQbaL4R-FYiOc51Nks5teUZhgaJpZM4Si2YZ>.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country
by U.S. News & World Report (2017-2018). Visit us online at
http://www.clevelandclinic.org for a complete listing of our services,
staff and locations. Confidentiality Note: This message is intended for use
only by the individual or entity to which it is addressed and may contain
information that is privileged, confidential, and exempt from disclosure
under applicable law. If the reader of this message is not the intended
recipient or the employee or agent responsible for delivering the message
to the intended recipient, you are hereby notified that any dissemination,
distribution or copying of this communication is strictly prohibited. If
you have received this communication in error, please contact the sender
immediately and destroy the material in its entirety, whether electronic or
hard copy. Thank you.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#56 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AE1pidgjzq9SV9YW1Is63NaIjtwNSMBOks5teUb2gaJpZM4Si2YZ>
.
from leafcutter.
seyfim
commented on September 19, 2024
Sorry for not being clear!
Yes those are the 2 classes but within each class I do a comparison like the following:
P14M3M4Wt_merged.sorted.filtered.bam (1) vs P14M3M4Mut_merged.sorted.filtered.bam (1)
Or
P40M3M4Wt_merged.sorted.filtered.bam (2) vs P40M3M4Wt_merged.sorted.filtered.bam (2)
I make sure to differentiate the different classes with their corresponding comparisons in my test.junc files and in my intron_diff files
On Mar 15, 2018, at 11:53 AM, goldenflaw <[email protected]<mailto:[email protected]>> wrote:
I'm still confused are the assignments as such:
P40M3M4Wt_merged.sorted.filtered.bam 2
P14M3M4Mut_merged.sorted.filtered.bam 1
P40M3M4Wt_merged.sorted.filtered.bam 2
P14M3M4Wt_merged.sorted.filtered.bam 1
P40M3M4Het_merged.sorted.filtered.bam 2
P14M3M4Het_merged.sorted.filtered.bam 1
On Wed, Mar 14, 2018 at 11:36 AM, seyfim ***@***.******@***.***>> wrote:
I have two sets (either P14M3M4 or P40M3M4) and the comparisons for each
set are sample1: Wt, Wt, Mut then sample 2: Mut, Het, Het respectively
On Mar 14, 2018, at 12:33 PM, goldenflaw ***@***.******@***.***><mailto:
***@***.******@***.***>>> wrote:
Thanks, but I'm not sure I understand? Which 3 samples are condition 1 and
which 3 are condition 2?
Best,
Yang
On Wed, Mar 14, 2018 at 11:21 AM, mh406910 ***@***.******@***.***><
***@***.***>> wrote:
> Hello,
>
> So after reviewing the files I did have the correct samples. The
> comparisons are as follows:
>
>
>
> P14M3M4Wt_merged.sorted.filtered.bam vs P14M3M4Mut_merged.sorted.
> filtered.bam
>
> P14M3M4Wt_merged.sorted.filtered.bam vs P14M3M4Het_merged.sorted.
> filtered.bam
>
> P14M3M4Mut_merged.sorted.filtered.bam . vs P14M3M4Het_merged.sorted.
> filtered.bam
>
> P40M3M4Wt_merged.sorted.filtered.bam vs P40M3M4Mut_merged.sorted.
> filtered.bam
>
> P40M3M4Wt_merged.sorted.filtered.bam vs P40M3M4Het_merged.sorted.
> filtered.bam
>
> P40M3M4Mut_merged.sorted.filtered.bam vs P40M3M4Het_merged.sorted.
> filtered.bam
>
>
> Thanks,
> Marilyn E. Seyfi
> Bioinformatics Technologist
> Cleveland Clinic Genomic Medicine Institute
> work email: ***@***.******@***.******@***.***>
> mobile: (740)-603-2131 <(740)%20603-2131> <(740)%20603-2131>
>
>
>
>
> ________________________________
> From: goldenflaw ***@***.******@***.******@***.***
com>>
> Sent: Tuesday, March 13, 2018 6:35 PM
>
> To: davidaknowles/leafcutter
> Cc: Seyfi, Marilyn; Comment
> Subject: Re: [davidaknowles/leafcutter] small sample size affecting
> cluster significance detection? (#56)
>
> These samples are from the leafcutter output that you gave me (
> test_perind_numers.counts.gz
> <https://github.com/davidaknowles/leafcutter/files/1797264/test_perind_
> numers.counts.gz>
> )
>
> On Tue, Mar 13, 2018 at 5:32 PM, mh406910 ***@***.******@***.***><
***@***.***>>
> wrote:
>
> > Well those are not correct.. It should be P14Wt or P40Wt (sample 1) vs
> > P14Mut or P40Mut (sample 2)... I included all comparisons in the .junc
> step
> > and the following intro cluster step --was that incorrect?
> >
> > Get Outlook for Android<https://aka.ms/ghei36>
> >
> > ________________________________
> > From: goldenflaw ***@***.******@***.***><mailto:
***@***.******@***.***>>>
> > Sent: Tuesday, March 13, 2018 6:27:23 PM
> >
> > To: davidaknowles/leafcutter
> > Cc: Seyfi, Marilyn; Comment
> > Subject: Re: [davidaknowles/leafcutter] small sample size affecting
> > cluster significance detection? (#56)
> >
> > I see that you have 6 samples:
> >
> > P40M3M4Wt_merged.sorted.filtered.bam P14M3M4Mut_merged.sorted.
> filtered.bam
> > P40M3M4Mut_merged.sorted.filtered.bam P14M3M4Wt_merged.sorted.
> filtered.bam
> > P40M3M4Het_merged.sorted.filtered.bam P14M3M4Het_merged.sorted.
> > filtered.bam
> >
> >
> > Could you tell me which ones are "condition 1" and which ones are
> > "condition 2".
> >
> > On Tue, Mar 13, 2018 at 5:25 PM, mh406910 ***@***.******@***.***><
***@***.***>>
> > wrote:
> >
> > > Just to clarify you mean the ban file? As well as the output from
rMATS
> > > and MISO with their highest delta pi value for the selected sample
> > > comparison?
> > >
> > > Get Outlook for Android<https://aka.ms/ghei36>
> > >
> > > ________________________________
> > > From: goldenflaw ***@***.******@***.***><mailto:
***@***.******@***.***>>>
> > > Sent: Tuesday, March 13, 2018 6:23:24 PM
> > >
> > > To: davidaknowles/leafcutter
> > > Cc: Seyfi, Marilyn; Comment
> > > Subject: Re: [davidaknowles/leafcutter] small sample size affecting
> > > cluster significance detection? (#56)
> > >
> > > Could you provide the correct mapping of samples to conditions? And
> your
> > > strongest "hit" from rMATS and or MISO.
> > >
> > > Best,
> > > Yang
> > >
> > > On Tue, Mar 13, 2018 at 5:21 PM, mh406910 ***@***.******@***.***><
***@***.***>>
> > > wrote:
> > >
> > > > Also when I run your program with the replicates unmerged as
separate
> > > > replicates I get the same error that there are no significant
> clusters.
> > > > MISO and rMATS both report otherwise.
> > > >
> > > > Get Outlook for Android<https://aka.ms/ghei36>
> > > >
> > > > ________________________________
> > > > From: goldenflaw ***@***.******@***.***><mailto:
***@***.******@***.***>>>
> > > > Sent: Tuesday, March 13, 2018 3:02:47 PM
> > > > To: davidaknowles/leafcutter
> > > > Cc: Seyfi, Marilyn; Comment
> > > > Subject: Re: [davidaknowles/leafcutter] small sample size
affecting
> > > > cluster significance detection? (#56)
> > > >
> > > > Your P14WTmut.txt file looks wrong, you only have 2 samples in
there.
> > > >
> > > > Best,
> > > > Yang
> > > >
> > > > On Fri, Mar 9, 2018 at 9:07 AM, Yang Li ***@***.******@***.***>
***@***.***>>
> wrote:
> > > >
> > > > > I will have a look at the whole thing.
> > > > >
> > > > > Best,
> > > > > Yang
> > > > >
> > > > > On Mar 9, 2018 8:54 AM, "seyfim" ***@***.******@***.***><
***@***.***>> wrote:
> > > > >
> > > > >> how do I just share one chromosome with you?
> > > > >>
> > > > >> —
> > > > >> You are receiving this because you were mentioned.
> > > > >> Reply to this email directly, view it on GitHub
> > > > >> <https://github.com/davidaknowles/leafcutter/
> > issues/56#issuecomment-
> > > > 371835036>,
> > > > >> or mute the thread
> > > > >> <https://github.com/notifications/unsubscribe-auth/
> > > > AE1piZqBGBpzf2cNNshOQCmtkfMdzzChks5tcpe2gaJpZM4Si2YZ>
> > > > >> .
> > > > >>
> > > > >
> > > >
> > > > —
> > > > You are receiving this because you commented.
> > > > Reply to this email directly, view it on GitHub<
https://github.com/
> > > > davidaknowles/leafcutter#56#issuecomment-372781944>, or
mute
> > the
> > > > thread<https://github.com/notifications/unsubscribe-auth/
> > > > AH0qV7HiNDq4nRYq6MBi9a1xWDnMNfEUks5teBfWgaJpZM4Si2YZ>.
> > > >
> > > > —
> > > > You are receiving this because you were mentioned.
> > > > Reply to this email directly, view it on GitHub
> > > > <https://github.com/davidaknowles/leafcutter/
issues/56#issuecomment-
> > > 372838727>,
> > > > or mute the thread
> > > > <https://github.com/notifications/unsubscribe-auth/AE1pif2tfb_
> > > R056uBWbmrOrB1zLXuxdoks5teEZOgaJpZM4Si2YZ>
> > > > .
> > > >
> > >
> > > —
> > > You are receiving this because you commented.
> > > Reply to this email directly, view it on GitHub<https://github.com/
> > > davidaknowles/leafcutter#56#issuecomment-372839266>, or mute
> the
> > > thread<https://github.com/notifications/unsubscribe-auth/
> > > AH0qV4a50BHXeGYRRfHWzlaqB1rvfmN4ks5teEbcgaJpZM4Si2YZ>.
> > >
> > > —
> > > You are receiving this because you were mentioned.
> > > Reply to this email directly, view it on GitHub
> > > <#56 (comment)-
> > 372839683>,
> > > or mute the thread
> > > <https://github.com/notifications/unsubscribe-auth/
> > AE1piXefiUjlA0HwvzOEvT5OynDQUxMiks5teEdOgaJpZM4Si2YZ>
> > > .
> > >
> >
> > —
> > You are receiving this because you commented.
> > Reply to this email directly, view it on GitHub<https://github.com/
> > davidaknowles/leafcutter#56#issuecomment-372840184>, or mute
the
> > thread<https://github.com/notifications/unsubscribe-auth/AH0qV7Aqc_
> > xXMWmaRAqFAffdAH88FYvWks5teEfKgaJpZM4Si2YZ>.
> >
> > —
> > You are receiving this because you were mentioned.
> > Reply to this email directly, view it on GitHub
> > <#56 (comment)-
> 372841413>,
> > or mute the thread
> > <https://github.com/notifications/unsubscribe-auth/
> AE1pifjojIveXOgnlLQb8BSregse9Dcvks5teEkNgaJpZM4Si2YZ>
> > .
> >
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub<https://github.com/
> davidaknowles/leafcutter#56#issuecomment-372842066>, or mute the
> thread<https://github.com/notifications/unsubscribe-auth/
> AH0qVyVeY6qZqaqwDsXLAfyjgplfknB6ks5teEmqgaJpZM4Si2YZ>.
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <#56 (comment)-
373083237>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AE1picyeYN0qgm8x_
1MbtBCWV5AT8eLNks5teUNwgaJpZM4Si2YZ>
> .
>
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub<https://github.com/
davidaknowles/leafcutter#56#issuecomment-373087793>, or mute the
thread<https://github.com/notifications/unsubscribe-
auth/AikLJbxBarvHE4PBpQbaL4R-FYiOc51Nks5teUZhgaJpZM4Si2YZ>.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country
by U.S. News & World Report (2017-2018). Visit us online at
http://www.clevelandclinic.org for a complete listing of our services,
staff and locations. Confidentiality Note: This message is intended for use
only by the individual or entity to which it is addressed and may contain
information that is privileged, confidential, and exempt from disclosure
under applicable law. If the reader of this message is not the intended
recipient or the employee or agent responsible for delivering the message
to the intended recipient, you are hereby notified that any dissemination,
distribution or copying of this communication is strictly prohibited. If
you have received this communication in error, please contact the sender
immediately and destroy the material in its entirety, whether electronic or
hard copy. Thank you.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#56 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AE1pidgjzq9SV9YW1Is63NaIjtwNSMBOks5teUb2gaJpZM4Si2YZ>
.
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub<#56 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AikLJUmD86LbwVjw_rwMERYtyO6Bixt0ks5teo6NgaJpZM4Si2YZ>.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
from leafcutter.
goldenflaw
commented on September 19, 2024
LeafCutter (and I believe the other tools that you used) does not support
paired samples. When I ran your test without pairing, I get some
significant hits.
Best,
Yang
…On Thu, Mar 15, 2018 at 11:49 AM, seyfim ***@***.***> wrote:
Sorry for not being clear!
Yes those are the 2 classes but within each class I do a comparison like
the following:
P14M3M4Wt_merged.sorted.filtered.bam (1) vs P14M3M4Mut_merged.sorted.filtered.bam
(1)
Or
P40M3M4Wt_merged.sorted.filtered.bam (2) vs P40M3M4Wt_merged.sorted.filtered.bam
(2)
I make sure to differentiate the different classes with their
corresponding comparisons in my test.junc files and in my intron_diff files
On Mar 15, 2018, at 11:53 AM, goldenflaw ***@***.***<mailto:
***@***.***>> wrote:
I'm still confused are the assignments as such:
P40M3M4Wt_merged.sorted.filtered.bam 2
P14M3M4Mut_merged.sorted.filtered.bam 1
P40M3M4Wt_merged.sorted.filtered.bam 2
P14M3M4Wt_merged.sorted.filtered.bam 1
P40M3M4Het_merged.sorted.filtered.bam 2
P14M3M4Het_merged.sorted.filtered.bam 1
On Wed, Mar 14, 2018 at 11:36 AM, seyfim ***@***.***<mailto:
***@***.***>> wrote:
> I have two sets (either P14M3M4 or P40M3M4) and the comparisons for each
> set are sample1: Wt, Wt, Mut then sample 2: Mut, Het, Het respectively
> On Mar 14, 2018, at 12:33 PM, goldenflaw ***@***.***<mail
***@***.***><mailto:
> ***@***.******@***.***>>> wrote:
>
> Thanks, but I'm not sure I understand? Which 3 samples are condition 1
and
> which 3 are condition 2?
> Best,
> Yang
>
> On Wed, Mar 14, 2018 at 11:21 AM, mh406910 ***@***.***
***@***.***><
> ***@***.***>> wrote:
>
> > Hello,
> >
> > So after reviewing the files I did have the correct samples. The
> > comparisons are as follows:
> >
> >
> >
> > P14M3M4Wt_merged.sorted.filtered.bam vs P14M3M4Mut_merged.sorted.
> > filtered.bam
> >
> > P14M3M4Wt_merged.sorted.filtered.bam vs P14M3M4Het_merged.sorted.
> > filtered.bam
> >
> > P14M3M4Mut_merged.sorted.filtered.bam . vs P14M3M4Het_merged.sorted.
> > filtered.bam
> >
> > P40M3M4Wt_merged.sorted.filtered.bam vs P40M3M4Mut_merged.sorted.
> > filtered.bam
> >
> > P40M3M4Wt_merged.sorted.filtered.bam vs P40M3M4Het_merged.sorted.
> > filtered.bam
> >
> > P40M3M4Mut_merged.sorted.filtered.bam vs P40M3M4Het_merged.sorted.
> > filtered.bam
> >
> >
> > Thanks,
> > Marilyn E. Seyfi
> > Bioinformatics Technologist
> > Cleveland Clinic Genomic Medicine Institute
> > work email: ***@***.******@***.***><mailto:
***@***.***>
> > mobile: (740)-603-2131 <(740)%20603-2131> <(740)%20603-2131>
<(740)%20603-2131>
> >
> >
> >
> >
> > ________________________________
> > From: goldenflaw ***@***.***<mailto:
***@***.******@***.***
> com>>
> > Sent: Tuesday, March 13, 2018 6:35 PM
> >
> > To: davidaknowles/leafcutter
> > Cc: Seyfi, Marilyn; Comment
> > Subject: Re: [davidaknowles/leafcutter] small sample size affecting
> > cluster significance detection? (#56)
> >
> > These samples are from the leafcutter output that you gave me (
> > test_perind_numers.counts.gz
> > <https://github.com/davidaknowles/leafcutter/files/1797264/t
est_perind_
> > numers.counts.gz>
> > )
> >
> > On Tue, Mar 13, 2018 at 5:32 PM, mh406910 ***@***.***
***@***.***><
> ***@***.***>>
> > wrote:
> >
> > > Well those are not correct.. It should be P14Wt or P40Wt (sample 1)
vs
> > > P14Mut or P40Mut (sample 2)... I included all comparisons in the
.junc
> > step
> > > and the following intro cluster step --was that incorrect?
> > >
> > > Get Outlook for Android<https://aka.ms/ghei36>
> > >
> > > ________________________________
> > > From: goldenflaw ***@***.***<mailto:
***@***.***><mailto:
> ***@***.******@***.***>>>
> > > Sent: Tuesday, March 13, 2018 6:27:23 PM
> > >
> > > To: davidaknowles/leafcutter
> > > Cc: Seyfi, Marilyn; Comment
> > > Subject: Re: [davidaknowles/leafcutter] small sample size affecting
> > > cluster significance detection? (#56)
> > >
> > > I see that you have 6 samples:
> > >
> > > P40M3M4Wt_merged.sorted.filtered.bam P14M3M4Mut_merged.sorted.
> > filtered.bam
> > > P40M3M4Mut_merged.sorted.filtered.bam P14M3M4Wt_merged.sorted.
> > filtered.bam
> > > P40M3M4Het_merged.sorted.filtered.bam P14M3M4Het_merged.sorted.
> > > filtered.bam
> > >
> > >
> > > Could you tell me which ones are "condition 1" and which ones are
> > > "condition 2".
> > >
> > > On Tue, Mar 13, 2018 at 5:25 PM, mh406910 ***@***.***
***@***.***><
> ***@***.***>>
> > > wrote:
> > >
> > > > Just to clarify you mean the ban file? As well as the output from
> rMATS
> > > > and MISO with their highest delta pi value for the selected sample
> > > > comparison?
> > > >
> > > > Get Outlook for Android<https://aka.ms/ghei36>
> > > >
> > > > ________________________________
> > > > From: goldenflaw ***@***.***<mailto:
***@***.***><mailto:
> ***@***.******@***.***>>>
> > > > Sent: Tuesday, March 13, 2018 6:23:24 PM
> > > >
> > > > To: davidaknowles/leafcutter
> > > > Cc: Seyfi, Marilyn; Comment
> > > > Subject: Re: [davidaknowles/leafcutter] small sample size
affecting
> > > > cluster significance detection? (#56)
> > > >
> > > > Could you provide the correct mapping of samples to conditions?
And
> > your
> > > > strongest "hit" from rMATS and or MISO.
> > > >
> > > > Best,
> > > > Yang
> > > >
> > > > On Tue, Mar 13, 2018 at 5:21 PM, mh406910 <
***@***.******@***.***><
> ***@***.***>>
> > > > wrote:
> > > >
> > > > > Also when I run your program with the replicates unmerged as
> separate
> > > > > replicates I get the same error that there are no significant
> > clusters.
> > > > > MISO and rMATS both report otherwise.
> > > > >
> > > > > Get Outlook for Android<https://aka.ms/ghei36>
> > > > >
> > > > > ________________________________
> > > > > From: goldenflaw ***@***.***<mailto:
***@***.***><mailto:
> ***@***.******@***.***>>>
> > > > > Sent: Tuesday, March 13, 2018 3:02:47 PM
> > > > > To: davidaknowles/leafcutter
> > > > > Cc: Seyfi, Marilyn; Comment
> > > > > Subject: Re: [davidaknowles/leafcutter] small sample size
> affecting
> > > > > cluster significance detection? (#56)
> > > > >
> > > > > Your P14WTmut.txt file looks wrong, you only have 2 samples in
> there.
> > > > >
> > > > > Best,
> > > > > Yang
> > > > >
> > > > > On Fri, Mar 9, 2018 at 9:07 AM, Yang Li ***@***.***
***@***.***>
> ***@***.***>>
> > wrote:
> > > > >
> > > > > > I will have a look at the whole thing.
> > > > > >
> > > > > > Best,
> > > > > > Yang
> > > > > >
> > > > > > On Mar 9, 2018 8:54 AM, "seyfim" ***@***.***
***@***.***><
> ***@***.***>> wrote:
> > > > > >
> > > > > >> how do I just share one chromosome with you?
> > > > > >>
> > > > > >> —
> > > > > >> You are receiving this because you were mentioned.
> > > > > >> Reply to this email directly, view it on GitHub
> > > > > >> <https://github.com/davidaknowles/leafcutter/
> > > issues/56#issuecomment-
> > > > > 371835036>,
> > > > > >> or mute the thread
> > > > > >> <https://github.com/notifications/unsubscribe-auth/
> > > > > AE1piZqBGBpzf2cNNshOQCmtkfMdzzChks5tcpe2gaJpZM4Si2YZ>
> > > > > >> .
> > > > > >>
> > > > > >
> > > > >
> > > > > —
> > > > > You are receiving this because you commented.
> > > > > Reply to this email directly, view it on GitHub<
> https://github.com/
> > > > > davidaknowles/leafcutter#56#issuecomment-372781944>, or
> mute
> > > the
> > > > > thread<https://github.com/notifications/unsubscribe-auth/
> > > > > AH0qV7HiNDq4nRYq6MBi9a1xWDnMNfEUks5teBfWgaJpZM4Si2YZ>.
> > > > >
> > > > > —
> > > > > You are receiving this because you were mentioned.
> > > > > Reply to this email directly, view it on GitHub
> > > > > <https://github.com/davidaknowles/leafcutter/
> issues/56#issuecomment-
> > > > 372838727>,
> > > > > or mute the thread
> > > > > <https://github.com/notifications/unsubscribe-auth/AE1pif2tfb_
> > > > R056uBWbmrOrB1zLXuxdoks5teEZOgaJpZM4Si2YZ>
> > > > > .
> > > > >
> > > >
> > > > —
> > > > You are receiving this because you commented.
> > > > Reply to this email directly, view it on GitHub<
https://github.com/
> > > > davidaknowles/leafcutter#56#issuecomment-372839266>, or
mute
> > the
> > > > thread<https://github.com/notifications/unsubscribe-auth/
> > > > AH0qV4a50BHXeGYRRfHWzlaqB1rvfmN4ks5teEbcgaJpZM4Si2YZ>.
> > > >
> > > > —
> > > > You are receiving this because you were mentioned.
> > > > Reply to this email directly, view it on GitHub
> > > > <#56 (comment)
comment-
> > > 372839683>,
> > > > or mute the thread
> > > > <https://github.com/notifications/unsubscribe-auth/
> > > AE1piXefiUjlA0HwvzOEvT5OynDQUxMiks5teEdOgaJpZM4Si2YZ>
> > > > .
> > > >
> > >
> > > —
> > > You are receiving this because you commented.
> > > Reply to this email directly, view it on GitHub<https://github.com/
> > > davidaknowles/leafcutter#56#issuecomment-372840184>, or mute
> the
> > > thread<https://github.com/notifications/unsubscribe-auth/AH0qV7Aqc_
> > > xXMWmaRAqFAffdAH88FYvWks5teEfKgaJpZM4Si2YZ>.
> > >
> > > —
> > > You are receiving this because you were mentioned.
> > > Reply to this email directly, view it on GitHub
> > > <#56 (comment)-
> > 372841413>,
> > > or mute the thread
> > > <https://github.com/notifications/unsubscribe-auth/
> > AE1pifjojIveXOgnlLQb8BSregse9Dcvks5teEkNgaJpZM4Si2YZ>
> > > .
> > >
> >
> > —
> > You are receiving this because you commented.
> > Reply to this email directly, view it on GitHub<https://github.com/
> > davidaknowles/leafcutter#56#issuecomment-372842066>, or mute
the
> > thread<https://github.com/notifications/unsubscribe-auth/
> > AH0qVyVeY6qZqaqwDsXLAfyjgplfknB6ks5teEmqgaJpZM4Si2YZ>.
> >
> > —
> > You are receiving this because you were mentioned.
> > Reply to this email directly, view it on GitHub
> > <#56 (comment)-
> 373083237>,
> > or mute the thread
> > <https://github.com/notifications/unsubscribe-auth/AE1picyeYN0qgm8x_
> 1MbtBCWV5AT8eLNks5teUNwgaJpZM4Si2YZ>
> > .
> >
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub<https://github.com/
> davidaknowles/leafcutter#56#issuecomment-373087793>, or mute the
> thread<https://github.com/notifications/unsubscribe-
> auth/AikLJbxBarvHE4PBpQbaL4R-FYiOc51Nks5teUZhgaJpZM4Si2YZ>.
>
>
> ===================================
>
>
> Please consider the environment before printing this e-mail
>
> Cleveland Clinic is currently ranked as the No. 2 hospital in the
country
> by U.S. News & World Report (2017-2018). Visit us online at
> http://www.clevelandclinic.org for a complete listing of our services,
> staff and locations. Confidentiality Note: This message is intended for
use
> only by the individual or entity to which it is addressed and may
contain
> information that is privileged, confidential, and exempt from disclosure
> under applicable law. If the reader of this message is not the intended
> recipient or the employee or agent responsible for delivering the
message
> to the intended recipient, you are hereby notified that any
dissemination,
> distribution or copying of this communication is strictly prohibited. If
> you have received this communication in error, please contact the sender
> immediately and destroy the material in its entirety, whether electronic
or
> hard copy. Thank you.
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <#56 (comment)
comment-373088665>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AE1pidgjz
q9SV9YW1Is63NaIjtwNSMBOks5teUb2gaJpZM4Si2YZ>
> .
>
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub<https://github.com/davi
daknowles/leafcutter/issues/56#issuecomment-373426027>, or mute the
thread<https://github.com/notifications/unsubscribe-auth/Aik
LJUmD86LbwVjw_rwMERYtyO6Bixt0ks5teo6NgaJpZM4Si2YZ>.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country
by U.S. News & World Report (2017-2018). Visit us online at
http://www.clevelandclinic.org for a complete listing of our services,
staff and locations. Confidentiality Note: This message is intended for use
only by the individual or entity to which it is addressed and may contain
information that is privileged, confidential, and exempt from disclosure
under applicable law. If the reader of this message is not the intended
recipient or the employee or agent responsible for delivering the message
to the intended recipient, you are hereby notified that any dissemination,
distribution or copying of this communication is strictly prohibited. If
you have received this communication in error, please contact the sender
immediately and destroy the material in its entirety, whether electronic or
hard copy. Thank you.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#56 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AE1piQRwlOQtSEbOoIORNeFr0Un8sXFlks5tepuigaJpZM4Si2YZ>
.
from leafcutter.
seyfim
commented on September 19, 2024
No, I specifically used commands for paired-end data in both rMATS and MISO.
So, basically I cannot use your tool?
On Mar 15, 2018, at 12:57 PM, goldenflaw <[email protected]<mailto:[email protected]>> wrote:
LeafCutter (and I believe the other tools that you used) does not support
paired samples. When I ran your test without pairing, I get some
significant hits.
Best,
Yang
On Thu, Mar 15, 2018 at 11:49 AM, seyfim ***@***.******@***.***>> wrote:
Sorry for not being clear!
Yes those are the 2 classes but within each class I do a comparison like
the following:
P14M3M4Wt_merged.sorted.filtered.bam (1) vs P14M3M4Mut_merged.sorted.filtered.bam
(1)
Or
P40M3M4Wt_merged.sorted.filtered.bam (2) vs P40M3M4Wt_merged.sorted.filtered.bam
(2)
I make sure to differentiate the different classes with their
corresponding comparisons in my test.junc files and in my intron_diff files
On Mar 15, 2018, at 11:53 AM, goldenflaw ***@***.******@***.***><mailto:
***@***.******@***.***>>> wrote:
I'm still confused are the assignments as such:
P40M3M4Wt_merged.sorted.filtered.bam 2
P14M3M4Mut_merged.sorted.filtered.bam 1
P40M3M4Wt_merged.sorted.filtered.bam 2
P14M3M4Wt_merged.sorted.filtered.bam 1
P40M3M4Het_merged.sorted.filtered.bam 2
P14M3M4Het_merged.sorted.filtered.bam 1
On Wed, Mar 14, 2018 at 11:36 AM, seyfim ***@***.******@***.***><mailto:
***@***.******@***.***>>> wrote:
> I have two sets (either P14M3M4 or P40M3M4) and the comparisons for each
> set are sample1: Wt, Wt, Mut then sample 2: Mut, Het, Het respectively
> On Mar 14, 2018, at 12:33 PM, goldenflaw ***@***.******@***.***><mail
***@***.******@***.***>><mailto:
> ***@***.******@***.******@***.***>>> wrote:
>
> Thanks, but I'm not sure I understand? Which 3 samples are condition 1
and
> which 3 are condition 2?
> Best,
> Yang
>
> On Wed, Mar 14, 2018 at 11:21 AM, mh406910 ***@***.******@***.***>
***@***.***><
> ***@***.***>> wrote:
>
> > Hello,
> >
> > So after reviewing the files I did have the correct samples. The
> > comparisons are as follows:
> >
> >
> >
> > P14M3M4Wt_merged.sorted.filtered.bam vs P14M3M4Mut_merged.sorted.
> > filtered.bam
> >
> > P14M3M4Wt_merged.sorted.filtered.bam vs P14M3M4Het_merged.sorted.
> > filtered.bam
> >
> > P14M3M4Mut_merged.sorted.filtered.bam . vs P14M3M4Het_merged.sorted.
> > filtered.bam
> >
> > P40M3M4Wt_merged.sorted.filtered.bam vs P40M3M4Mut_merged.sorted.
> > filtered.bam
> >
> > P40M3M4Wt_merged.sorted.filtered.bam vs P40M3M4Het_merged.sorted.
> > filtered.bam
> >
> > P40M3M4Mut_merged.sorted.filtered.bam vs P40M3M4Het_merged.sorted.
> > filtered.bam
> >
> >
> > Thanks,
> > Marilyn E. Seyfi
> > Bioinformatics Technologist
> > Cleveland Clinic Genomic Medicine Institute
> > work email: ***@***.******@***.******@***.***><mailto:
***@***.******@***.***>>
> > mobile: (740)-603-2131 <(740)%20603-2131> <(740)%20603-2131>
<(740)%20603-2131>
> >
> >
> >
> >
> > ________________________________
> > From: goldenflaw ***@***.******@***.***><mailto:
***@***.******@***.******@***.***
> com>>
> > Sent: Tuesday, March 13, 2018 6:35 PM
> >
> > To: davidaknowles/leafcutter
> > Cc: Seyfi, Marilyn; Comment
> > Subject: Re: [davidaknowles/leafcutter] small sample size affecting
> > cluster significance detection? (#56)
> >
> > These samples are from the leafcutter output that you gave me (
> > test_perind_numers.counts.gz
> > <https://github.com/davidaknowles/leafcutter/files/1797264/t
est_perind_
> > numers.counts.gz>
> > )
> >
> > On Tue, Mar 13, 2018 at 5:32 PM, mh406910 ***@***.******@***.***>
***@***.***><
> ***@***.***>>
> > wrote:
> >
> > > Well those are not correct.. It should be P14Wt or P40Wt (sample 1)
vs
> > > P14Mut or P40Mut (sample 2)... I included all comparisons in the
.junc
> > step
> > > and the following intro cluster step --was that incorrect?
> > >
> > > Get Outlook for Android<https://aka.ms/ghei36>
> > >
> > > ________________________________
> > > From: goldenflaw ***@***.******@***.***><mailto:
***@***.******@***.***>><mailto:
> ***@***.******@***.******@***.***>>>
> > > Sent: Tuesday, March 13, 2018 6:27:23 PM
> > >
> > > To: davidaknowles/leafcutter
> > > Cc: Seyfi, Marilyn; Comment
> > > Subject: Re: [davidaknowles/leafcutter] small sample size affecting
> > > cluster significance detection? (#56)
> > >
> > > I see that you have 6 samples:
> > >
> > > P40M3M4Wt_merged.sorted.filtered.bam P14M3M4Mut_merged.sorted.
> > filtered.bam
> > > P40M3M4Mut_merged.sorted.filtered.bam P14M3M4Wt_merged.sorted.
> > filtered.bam
> > > P40M3M4Het_merged.sorted.filtered.bam P14M3M4Het_merged.sorted.
> > > filtered.bam
> > >
> > >
> > > Could you tell me which ones are "condition 1" and which ones are
> > > "condition 2".
> > >
> > > On Tue, Mar 13, 2018 at 5:25 PM, mh406910 ***@***.******@***.***>
***@***.***><
> ***@***.***>>
> > > wrote:
> > >
> > > > Just to clarify you mean the ban file? As well as the output from
> rMATS
> > > > and MISO with their highest delta pi value for the selected sample
> > > > comparison?
> > > >
> > > > Get Outlook for Android<https://aka.ms/ghei36>
> > > >
> > > > ________________________________
> > > > From: goldenflaw ***@***.******@***.***><mailto:
***@***.******@***.***>><mailto:
> ***@***.******@***.******@***.***>>>
> > > > Sent: Tuesday, March 13, 2018 6:23:24 PM
> > > >
> > > > To: davidaknowles/leafcutter
> > > > Cc: Seyfi, Marilyn; Comment
> > > > Subject: Re: [davidaknowles/leafcutter] small sample size
affecting
> > > > cluster significance detection? (#56)
> > > >
> > > > Could you provide the correct mapping of samples to conditions?
And
> > your
> > > > strongest "hit" from rMATS and or MISO.
> > > >
> > > > Best,
> > > > Yang
> > > >
> > > > On Tue, Mar 13, 2018 at 5:21 PM, mh406910 <
***@***.******@***.******@***.***><
> ***@***.***>>
> > > > wrote:
> > > >
> > > > > Also when I run your program with the replicates unmerged as
> separate
> > > > > replicates I get the same error that there are no significant
> > clusters.
> > > > > MISO and rMATS both report otherwise.
> > > > >
> > > > > Get Outlook for Android<https://aka.ms/ghei36>
> > > > >
> > > > > ________________________________
> > > > > From: goldenflaw ***@***.******@***.***><mailto:
***@***.******@***.***>><mailto:
> ***@***.******@***.******@***.***>>>
> > > > > Sent: Tuesday, March 13, 2018 3:02:47 PM
> > > > > To: davidaknowles/leafcutter
> > > > > Cc: Seyfi, Marilyn; Comment
> > > > > Subject: Re: [davidaknowles/leafcutter] small sample size
> affecting
> > > > > cluster significance detection? (#56)
> > > > >
> > > > > Your P14WTmut.txt file looks wrong, you only have 2 samples in
> there.
> > > > >
> > > > > Best,
> > > > > Yang
> > > > >
> > > > > On Fri, Mar 9, 2018 at 9:07 AM, Yang Li ***@***.******@***.***>
***@***.***>
> ***@***.***>>
> > wrote:
> > > > >
> > > > > > I will have a look at the whole thing.
> > > > > >
> > > > > > Best,
> > > > > > Yang
> > > > > >
> > > > > > On Mar 9, 2018 8:54 AM, "seyfim" ***@***.******@***.***>
***@***.***><
> ***@***.***>> wrote:
> > > > > >
> > > > > >> how do I just share one chromosome with you?
> > > > > >>
> > > > > >> —
> > > > > >> You are receiving this because you were mentioned.
> > > > > >> Reply to this email directly, view it on GitHub
> > > > > >> <https://github.com/davidaknowles/leafcutter/
> > > issues/56#issuecomment-
> > > > > 371835036>,
> > > > > >> or mute the thread
> > > > > >> <https://github.com/notifications/unsubscribe-auth/
> > > > > AE1piZqBGBpzf2cNNshOQCmtkfMdzzChks5tcpe2gaJpZM4Si2YZ>
> > > > > >> .
> > > > > >>
> > > > > >
> > > > >
> > > > > —
> > > > > You are receiving this because you commented.
> > > > > Reply to this email directly, view it on GitHub<
> https://github.com/
> > > > > davidaknowles/leafcutter#56#issuecomment-372781944>, or
> mute
> > > the
> > > > > thread<https://github.com/notifications/unsubscribe-auth/
> > > > > AH0qV7HiNDq4nRYq6MBi9a1xWDnMNfEUks5teBfWgaJpZM4Si2YZ>.
> > > > >
> > > > > —
> > > > > You are receiving this because you were mentioned.
> > > > > Reply to this email directly, view it on GitHub
> > > > > <https://github.com/davidaknowles/leafcutter/
> issues/56#issuecomment-
> > > > 372838727>,
> > > > > or mute the thread
> > > > > <https://github.com/notifications/unsubscribe-auth/AE1pif2tfb_
> > > > R056uBWbmrOrB1zLXuxdoks5teEZOgaJpZM4Si2YZ>
> > > > > .
> > > > >
> > > >
> > > > —
> > > > You are receiving this because you commented.
> > > > Reply to this email directly, view it on GitHub<
https://github.com/
> > > > davidaknowles/leafcutter#56#issuecomment-372839266>, or
mute
> > the
> > > > thread<https://github.com/notifications/unsubscribe-auth/
> > > > AH0qV4a50BHXeGYRRfHWzlaqB1rvfmN4ks5teEbcgaJpZM4Si2YZ>.
> > > >
> > > > —
> > > > You are receiving this because you were mentioned.
> > > > Reply to this email directly, view it on GitHub
> > > > <#56 (comment)
comment-
> > > 372839683>,
> > > > or mute the thread
> > > > <https://github.com/notifications/unsubscribe-auth/
> > > AE1piXefiUjlA0HwvzOEvT5OynDQUxMiks5teEdOgaJpZM4Si2YZ>
> > > > .
> > > >
> > >
> > > —
> > > You are receiving this because you commented.
> > > Reply to this email directly, view it on GitHub<https://github.com/
> > > davidaknowles/leafcutter#56#issuecomment-372840184>, or mute
> the
> > > thread<https://github.com/notifications/unsubscribe-auth/AH0qV7Aqc_
> > > xXMWmaRAqFAffdAH88FYvWks5teEfKgaJpZM4Si2YZ>.
> > >
> > > —
> > > You are receiving this because you were mentioned.
> > > Reply to this email directly, view it on GitHub
> > > <#56 (comment)-
> > 372841413>,
> > > or mute the thread
> > > <https://github.com/notifications/unsubscribe-auth/
> > AE1pifjojIveXOgnlLQb8BSregse9Dcvks5teEkNgaJpZM4Si2YZ>
> > > .
> > >
> >
> > —
> > You are receiving this because you commented.
> > Reply to this email directly, view it on GitHub<https://github.com/
> > davidaknowles/leafcutter#56#issuecomment-372842066>, or mute
the
> > thread<https://github.com/notifications/unsubscribe-auth/
> > AH0qVyVeY6qZqaqwDsXLAfyjgplfknB6ks5teEmqgaJpZM4Si2YZ>.
> >
> > —
> > You are receiving this because you were mentioned.
> > Reply to this email directly, view it on GitHub
> > <#56 (comment)-
> 373083237>,
> > or mute the thread
> > <https://github.com/notifications/unsubscribe-auth/AE1picyeYN0qgm8x_
> 1MbtBCWV5AT8eLNks5teUNwgaJpZM4Si2YZ>
> > .
> >
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub<https://github.com/
> davidaknowles/leafcutter#56#issuecomment-373087793>, or mute the
> thread<https://github.com/notifications/unsubscribe-
> auth/AikLJbxBarvHE4PBpQbaL4R-FYiOc51Nks5teUZhgaJpZM4Si2YZ>.
>
>
> ===================================
>
>
> Please consider the environment before printing this e-mail
>
> Cleveland Clinic is currently ranked as the No. 2 hospital in the
country
> by U.S. News & World Report (2017-2018). Visit us online at
> http://www.clevelandclinic.org for a complete listing of our services,
> staff and locations. Confidentiality Note: This message is intended for
use
> only by the individual or entity to which it is addressed and may
contain
> information that is privileged, confidential, and exempt from disclosure
> under applicable law. If the reader of this message is not the intended
> recipient or the employee or agent responsible for delivering the
message
> to the intended recipient, you are hereby notified that any
dissemination,
> distribution or copying of this communication is strictly prohibited. If
> you have received this communication in error, please contact the sender
> immediately and destroy the material in its entirety, whether electronic
or
> hard copy. Thank you.
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <#56 (comment)
comment-373088665>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AE1pidgjz
q9SV9YW1Is63NaIjtwNSMBOks5teUb2gaJpZM4Si2YZ>
> .
>
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub<https://github.com/davi
daknowles/leafcutter/issues/56#issuecomment-373426027>, or mute the
thread<https://github.com/notifications/unsubscribe-auth/Aik
LJUmD86LbwVjw_rwMERYtyO6Bixt0ks5teo6NgaJpZM4Si2YZ>.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country
by U.S. News & World Report (2017-2018). Visit us online at
http://www.clevelandclinic.org for a complete listing of our services,
staff and locations. Confidentiality Note: This message is intended for use
only by the individual or entity to which it is addressed and may contain
information that is privileged, confidential, and exempt from disclosure
under applicable law. If the reader of this message is not the intended
recipient or the employee or agent responsible for delivering the message
to the intended recipient, you are hereby notified that any dissemination,
distribution or copying of this communication is strictly prohibited. If
you have received this communication in error, please contact the sender
immediately and destroy the material in its entirety, whether electronic or
hard copy. Thank you.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#56 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AE1piQRwlOQtSEbOoIORNeFr0Un8sXFlks5tepuigaJpZM4Si2YZ>
.
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub<#56 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AikLJRJjEQjxZtUsXPvFOXwhZhiGL6Imks5tep1ygaJpZM4Si2YZ>.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
from leafcutter.
goldenflaw
commented on September 19, 2024
"Paired-end" data does not refer to paired samples comparisons, it refers
to paired-end reads. Please have a look at the output files when you do not
match up your samples for comparisons.
Best,
Yang
…On Thu, Mar 15, 2018 at 11:58 AM, seyfim ***@***.***> wrote:
No, I specifically used commands for paired-end data in both rMATS and
MISO.
So, basically I cannot use your tool?
On Mar 15, 2018, at 12:57 PM, goldenflaw ***@***.***<mailto:
***@***.***>> wrote:
LeafCutter (and I believe the other tools that you used) does not support
paired samples. When I ran your test without pairing, I get some
significant hits.
Best,
Yang
On Thu, Mar 15, 2018 at 11:49 AM, seyfim ***@***.***<mailto:
***@***.***>> wrote:
> Sorry for not being clear!
> Yes those are the 2 classes but within each class I do a comparison like
> the following:
> P14M3M4Wt_merged.sorted.filtered.bam (1) vs
P14M3M4Mut_merged.sorted.filtered.bam
> (1)
> Or
> P40M3M4Wt_merged.sorted.filtered.bam (2) vs
P40M3M4Wt_merged.sorted.filtered.bam
> (2)
>
> I make sure to differentiate the different classes with their
> corresponding comparisons in my test.junc files and in my intron_diff
files
>
> On Mar 15, 2018, at 11:53 AM, goldenflaw ***@***.***<mail
***@***.***><mailto:
> ***@***.******@***.***>>> wrote:
>
> I'm still confused are the assignments as such:
>
> P40M3M4Wt_merged.sorted.filtered.bam 2
>
> P14M3M4Mut_merged.sorted.filtered.bam 1
>
> P40M3M4Wt_merged.sorted.filtered.bam 2
>
> P14M3M4Wt_merged.sorted.filtered.bam 1
>
> P40M3M4Het_merged.sorted.filtered.bam 2
>
> P14M3M4Het_merged.sorted.filtered.bam 1
>
>
>
>
> On Wed, Mar 14, 2018 at 11:36 AM, seyfim ***@***.***<mail
***@***.***><mailto:
> ***@***.******@***.***>>> wrote:
>
> > I have two sets (either P14M3M4 or P40M3M4) and the comparisons for
each
> > set are sample1: Wt, Wt, Mut then sample 2: Mut, Het, Het respectively
> > On Mar 14, 2018, at 12:33 PM, goldenflaw ***@***.***
***@***.***><mail
> ***@***.******@***.***>><mailto:
> > ***@***.******@***.***><mailto:
***@***.***>>> wrote:
> >
> > Thanks, but I'm not sure I understand? Which 3 samples are condition 1
> and
> > which 3 are condition 2?
> > Best,
> > Yang
> >
> > On Wed, Mar 14, 2018 at 11:21 AM, mh406910 ***@***.***
***@***.***>
> ***@***.***><
> > ***@***.***>> wrote:
> >
> > > Hello,
> > >
> > > So after reviewing the files I did have the correct samples. The
> > > comparisons are as follows:
> > >
> > >
> > >
> > > P14M3M4Wt_merged.sorted.filtered.bam vs P14M3M4Mut_merged.sorted.
> > > filtered.bam
> > >
> > > P14M3M4Wt_merged.sorted.filtered.bam vs P14M3M4Het_merged.sorted.
> > > filtered.bam
> > >
> > > P14M3M4Mut_merged.sorted.filtered.bam . vs
P14M3M4Het_merged.sorted.
> > > filtered.bam
> > >
> > > P40M3M4Wt_merged.sorted.filtered.bam vs P40M3M4Mut_merged.sorted.
> > > filtered.bam
> > >
> > > P40M3M4Wt_merged.sorted.filtered.bam vs P40M3M4Het_merged.sorted.
> > > filtered.bam
> > >
> > > P40M3M4Mut_merged.sorted.filtered.bam vs P40M3M4Het_merged.sorted.
> > > filtered.bam
> > >
> > >
> > > Thanks,
> > > Marilyn E. Seyfi
> > > Bioinformatics Technologist
> > > Cleveland Clinic Genomic Medicine Institute
> > > work email: ***@***.******@***.***><mailto:
***@***.***><mailto:
> ***@***.******@***.***>>
> > > mobile: (740)-603-2131 <(740)%20603-2131> <(740)%20603-2131>
<(740)%20603-2131>
> <(740)%20603-2131>
> > >
> > >
> > >
> > >
> > > ________________________________
> > > From: goldenflaw ***@***.***<mailto:
***@***.***><mailto:
> ***@***.******@***.***>><mailto:
***@***.***
> > com>>
> > > Sent: Tuesday, March 13, 2018 6:35 PM
> > >
> > > To: davidaknowles/leafcutter
> > > Cc: Seyfi, Marilyn; Comment
> > > Subject: Re: [davidaknowles/leafcutter] small sample size affecting
> > > cluster significance detection? (#56)
> > >
> > > These samples are from the leafcutter output that you gave me (
> > > test_perind_numers.counts.gz
> > > <https://github.com/davidaknowles/leafcutter/files/1797264/t
> est_perind_
> > > numers.counts.gz>
> > > )
> > >
> > > On Tue, Mar 13, 2018 at 5:32 PM, mh406910 ***@***.***
***@***.***>
> ***@***.***><
> > ***@***.***>>
> > > wrote:
> > >
> > > > Well those are not correct.. It should be P14Wt or P40Wt (sample
1)
> vs
> > > > P14Mut or P40Mut (sample 2)... I included all comparisons in the
> .junc
> > > step
> > > > and the following intro cluster step --was that incorrect?
> > > >
> > > > Get Outlook for Android<https://aka.ms/ghei36>
> > > >
> > > > ________________________________
> > > > From: goldenflaw ***@***.***<mailto:
***@***.***><mailto:
> ***@***.******@***.***>><mailto:
> > ***@***.******@***.***><mailto:
***@***.***>>>
> > > > Sent: Tuesday, March 13, 2018 6:27:23 PM
> > > >
> > > > To: davidaknowles/leafcutter
> > > > Cc: Seyfi, Marilyn; Comment
> > > > Subject: Re: [davidaknowles/leafcutter] small sample size
affecting
> > > > cluster significance detection? (#56)
> > > >
> > > > I see that you have 6 samples:
> > > >
> > > > P40M3M4Wt_merged.sorted.filtered.bam P14M3M4Mut_merged.sorted.
> > > filtered.bam
> > > > P40M3M4Mut_merged.sorted.filtered.bam P14M3M4Wt_merged.sorted.
> > > filtered.bam
> > > > P40M3M4Het_merged.sorted.filtered.bam P14M3M4Het_merged.sorted.
> > > > filtered.bam
> > > >
> > > >
> > > > Could you tell me which ones are "condition 1" and which ones are
> > > > "condition 2".
> > > >
> > > > On Tue, Mar 13, 2018 at 5:25 PM, mh406910 <
***@***.******@***.***>
> ***@***.***><
> > ***@***.***>>
> > > > wrote:
> > > >
> > > > > Just to clarify you mean the ban file? As well as the output
from
> > rMATS
> > > > > and MISO with their highest delta pi value for the selected
sample
> > > > > comparison?
> > > > >
> > > > > Get Outlook for Android<https://aka.ms/ghei36>
> > > > >
> > > > > ________________________________
> > > > > From: goldenflaw ***@***.***<mailto:
***@***.***><mailto:
> ***@***.******@***.***>><mailto:
> > ***@***.******@***.***><mailto:
***@***.***>>>
> > > > > Sent: Tuesday, March 13, 2018 6:23:24 PM
> > > > >
> > > > > To: davidaknowles/leafcutter
> > > > > Cc: Seyfi, Marilyn; Comment
> > > > > Subject: Re: [davidaknowles/leafcutter] small sample size
> affecting
> > > > > cluster significance detection? (#56)
> > > > >
> > > > > Could you provide the correct mapping of samples to conditions?
> And
> > > your
> > > > > strongest "hit" from rMATS and or MISO.
> > > > >
> > > > > Best,
> > > > > Yang
> > > > >
> > > > > On Tue, Mar 13, 2018 at 5:21 PM, mh406910 <
> ***@***.******@***.***><mailto:
***@***.***><
> > ***@***.***>>
> > > > > wrote:
> > > > >
> > > > > > Also when I run your program with the replicates unmerged as
> > separate
> > > > > > replicates I get the same error that there are no significant
> > > clusters.
> > > > > > MISO and rMATS both report otherwise.
> > > > > >
> > > > > > Get Outlook for Android<https://aka.ms/ghei36>
> > > > > >
> > > > > > ________________________________
> > > > > > From: goldenflaw ***@***.***<mailto:
***@***.***><mailto:
> ***@***.******@***.***>><mailto:
> > ***@***.******@***.***><mailto:
***@***.***>>>
> > > > > > Sent: Tuesday, March 13, 2018 3:02:47 PM
> > > > > > To: davidaknowles/leafcutter
> > > > > > Cc: Seyfi, Marilyn; Comment
> > > > > > Subject: Re: [davidaknowles/leafcutter] small sample size
> > affecting
> > > > > > cluster significance detection? (#56)
> > > > > >
> > > > > > Your P14WTmut.txt file looks wrong, you only have 2 samples in
> > there.
> > > > > >
> > > > > > Best,
> > > > > > Yang
> > > > > >
> > > > > > On Fri, Mar 9, 2018 at 9:07 AM, Yang Li ***@***.***
***@***.***>
> ***@***.***>
> > ***@***.***>>
> > > wrote:
> > > > > >
> > > > > > > I will have a look at the whole thing.
> > > > > > >
> > > > > > > Best,
> > > > > > > Yang
> > > > > > >
> > > > > > > On Mar 9, 2018 8:54 AM, "seyfim" ***@***.***
***@***.***>
> ***@***.***><
> > ***@***.***>> wrote:
> > > > > > >
> > > > > > >> how do I just share one chromosome with you?
> > > > > > >>
> > > > > > >> —
> > > > > > >> You are receiving this because you were mentioned.
> > > > > > >> Reply to this email directly, view it on GitHub
> > > > > > >> <https://github.com/davidaknowles/leafcutter/
> > > > issues/56#issuecomment-
> > > > > > 371835036>,
> > > > > > >> or mute the thread
> > > > > > >> <https://github.com/notifications/unsubscribe-auth/
> > > > > > AE1piZqBGBpzf2cNNshOQCmtkfMdzzChks5tcpe2gaJpZM4Si2YZ>
> > > > > > >> .
> > > > > > >>
> > > > > > >
> > > > > >
> > > > > > —
> > > > > > You are receiving this because you commented.
> > > > > > Reply to this email directly, view it on GitHub<
> > https://github.com/
> > > > > > davidaknowles/leafcutter#56#issuecomment-372781944>,
or
> > mute
> > > > the
> > > > > > thread<https://github.com/notifications/unsubscribe-auth/
> > > > > > AH0qV7HiNDq4nRYq6MBi9a1xWDnMNfEUks5teBfWgaJpZM4Si2YZ>.
> > > > > >
> > > > > > —
> > > > > > You are receiving this because you were mentioned.
> > > > > > Reply to this email directly, view it on GitHub
> > > > > > <https://github.com/davidaknowles/leafcutter/
> > issues/56#issuecomment-
> > > > > 372838727>,
> > > > > > or mute the thread
> > > > > > <https://github.com/notifications/unsubscribe-auth/AE1pif2tfb_
> > > > > R056uBWbmrOrB1zLXuxdoks5teEZOgaJpZM4Si2YZ>
> > > > > > .
> > > > > >
> > > > >
> > > > > —
> > > > > You are receiving this because you commented.
> > > > > Reply to this email directly, view it on GitHub<
> https://github.com/
> > > > > davidaknowles/leafcutter#56#issuecomment-372839266>, or
> mute
> > > the
> > > > > thread<https://github.com/notifications/unsubscribe-auth/
> > > > > AH0qV4a50BHXeGYRRfHWzlaqB1rvfmN4ks5teEbcgaJpZM4Si2YZ>.
> > > > >
> > > > > —
> > > > > You are receiving this because you were mentioned.
> > > > > Reply to this email directly, view it on GitHub
> > > > > <#56 (comment)
> comment-
> > > > 372839683>,
> > > > > or mute the thread
> > > > > <https://github.com/notifications/unsubscribe-auth/
> > > > AE1piXefiUjlA0HwvzOEvT5OynDQUxMiks5teEdOgaJpZM4Si2YZ>
> > > > > .
> > > > >
> > > >
> > > > —
> > > > You are receiving this because you commented.
> > > > Reply to this email directly, view it on GitHub<
https://github.com/
> > > > davidaknowles/leafcutter#56#issuecomment-372840184>, or
mute
> > the
> > > > thread<https://github.com/notifications/unsubscribe-auth/AH0
qV7Aqc_
> > > > xXMWmaRAqFAffdAH88FYvWks5teEfKgaJpZM4Si2YZ>.
> > > >
> > > > —
> > > > You are receiving this because you were mentioned.
> > > > Reply to this email directly, view it on GitHub
> > > > <#56 (comment)
comment-
> > > 372841413>,
> > > > or mute the thread
> > > > <https://github.com/notifications/unsubscribe-auth/
> > > AE1pifjojIveXOgnlLQb8BSregse9Dcvks5teEkNgaJpZM4Si2YZ>
> > > > .
> > > >
> > >
> > > —
> > > You are receiving this because you commented.
> > > Reply to this email directly, view it on GitHub<https://github.com/
> > > davidaknowles/leafcutter#56#issuecomment-372842066>, or mute
> the
> > > thread<https://github.com/notifications/unsubscribe-auth/
> > > AH0qVyVeY6qZqaqwDsXLAfyjgplfknB6ks5teEmqgaJpZM4Si2YZ>.
> > >
> > > —
> > > You are receiving this because you were mentioned.
> > > Reply to this email directly, view it on GitHub
> > > <#56 (comment)-
> > 373083237>,
> > > or mute the thread
> > > <https://github.com/notifications/unsubscribe-auth/AE1picyeYN0qgm8x_
> > 1MbtBCWV5AT8eLNks5teUNwgaJpZM4Si2YZ>
> > > .
> > >
> >
> > —
> > You are receiving this because you authored the thread.
> > Reply to this email directly, view it on GitHub<https://github.com/
> > davidaknowles/leafcutter#56#issuecomment-373087793>, or mute
the
> > thread<https://github.com/notifications/unsubscribe-
> > auth/AikLJbxBarvHE4PBpQbaL4R-FYiOc51Nks5teUZhgaJpZM4Si2YZ>.
> >
> >
> > ===================================
> >
> >
> > Please consider the environment before printing this e-mail
> >
> > Cleveland Clinic is currently ranked as the No. 2 hospital in the
> country
> > by U.S. News & World Report (2017-2018). Visit us online at
> > http://www.clevelandclinic.org for a complete listing of our
services,
> > staff and locations. Confidentiality Note: This message is intended
for
> use
> > only by the individual or entity to which it is addressed and may
> contain
> > information that is privileged, confidential, and exempt from
disclosure
> > under applicable law. If the reader of this message is not the
intended
> > recipient or the employee or agent responsible for delivering the
> message
> > to the intended recipient, you are hereby notified that any
> dissemination,
> > distribution or copying of this communication is strictly prohibited.
If
> > you have received this communication in error, please contact the
sender
> > immediately and destroy the material in its entirety, whether
electronic
> or
> > hard copy. Thank you.
> >
> > —
> > You are receiving this because you were mentioned.
> > Reply to this email directly, view it on GitHub
> > <#56 (comment)
> comment-373088665>,
> > or mute the thread
> > <https://github.com/notifications/unsubscribe-auth/AE1pidgjz
> q9SV9YW1Is63NaIjtwNSMBOks5teUb2gaJpZM4Si2YZ>
> > .
> >
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub<https://github.com/davi
> daknowles/leafcutter/issues/56#issuecomment-373426027>, or mute the
> thread<https://github.com/notifications/unsubscribe-auth/Aik
> LJUmD86LbwVjw_rwMERYtyO6Bixt0ks5teo6NgaJpZM4Si2YZ>.
>
>
> ===================================
>
>
> Please consider the environment before printing this e-mail
>
> Cleveland Clinic is currently ranked as the No. 2 hospital in the
country
> by U.S. News & World Report (2017-2018). Visit us online at
> http://www.clevelandclinic.org for a complete listing of our services,
> staff and locations. Confidentiality Note: This message is intended for
use
> only by the individual or entity to which it is addressed and may
contain
> information that is privileged, confidential, and exempt from disclosure
> under applicable law. If the reader of this message is not the intended
> recipient or the employee or agent responsible for delivering the
message
> to the intended recipient, you are hereby notified that any
dissemination,
> distribution or copying of this communication is strictly prohibited. If
> you have received this communication in error, please contact the sender
> immediately and destroy the material in its entirety, whether electronic
or
> hard copy. Thank you.
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <#56 (comment)
comment-373445540>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AE1piQRwl
OQtSEbOoIORNeFr0Un8sXFlks5tepuigaJpZM4Si2YZ>
> .
>
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub<https://github.com/davi
daknowles/leafcutter/issues/56#issuecomment-373448275>, or mute the
thread<https://github.com/notifications/unsubscribe-auth/Aik
LJRJjEQjxZtUsXPvFOXwhZhiGL6Imks5tep1ygaJpZM4Si2YZ>.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country
by U.S. News & World Report (2017-2018). Visit us online at
http://www.clevelandclinic.org for a complete listing of our services,
staff and locations. Confidentiality Note: This message is intended for use
only by the individual or entity to which it is addressed and may contain
information that is privileged, confidential, and exempt from disclosure
under applicable law. If the reader of this message is not the intended
recipient or the employee or agent responsible for delivering the message
to the intended recipient, you are hereby notified that any dissemination,
distribution or copying of this communication is strictly prohibited. If
you have received this communication in error, please contact the sender
immediately and destroy the material in its entirety, whether electronic or
hard copy. Thank you.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#56 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AE1piQx0dpuNbNOdXk8aKGXqe3Y7Ltvnks5tep3SgaJpZM4Si2YZ>
.
from leafcutter.
seyfim
commented on September 19, 2024
I know what that means, I have paired end sequencing reads...
On Mar 15, 2018, at 1:02 PM, goldenflaw <[email protected]<mailto:[email protected]>> wrote:
"Paired-end" data does not refer to paired samples comparisons, it refers
to paired-end reads. Please have a look at the output files when you do not
match up your samples for comparisons.
Best,
Yang
On Thu, Mar 15, 2018 at 11:58 AM, seyfim ***@***.******@***.***>> wrote:
No, I specifically used commands for paired-end data in both rMATS and
MISO.
So, basically I cannot use your tool?
On Mar 15, 2018, at 12:57 PM, goldenflaw ***@***.******@***.***><mailto:
***@***.******@***.***>>> wrote:
LeafCutter (and I believe the other tools that you used) does not support
paired samples. When I ran your test without pairing, I get some
significant hits.
Best,
Yang
On Thu, Mar 15, 2018 at 11:49 AM, seyfim ***@***.******@***.***><mailto:
***@***.******@***.***>>> wrote:
> Sorry for not being clear!
> Yes those are the 2 classes but within each class I do a comparison like
> the following:
> P14M3M4Wt_merged.sorted.filtered.bam (1) vs
P14M3M4Mut_merged.sorted.filtered.bam
> (1)
> Or
> P40M3M4Wt_merged.sorted.filtered.bam (2) vs
P40M3M4Wt_merged.sorted.filtered.bam
> (2)
>
> I make sure to differentiate the different classes with their
> corresponding comparisons in my test.junc files and in my intron_diff
files
>
> On Mar 15, 2018, at 11:53 AM, goldenflaw ***@***.******@***.***><mail
***@***.******@***.***>><mailto:
> ***@***.******@***.******@***.***>>> wrote:
>
> I'm still confused are the assignments as such:
>
> P40M3M4Wt_merged.sorted.filtered.bam 2
>
> P14M3M4Mut_merged.sorted.filtered.bam 1
>
> P40M3M4Wt_merged.sorted.filtered.bam 2
>
> P14M3M4Wt_merged.sorted.filtered.bam 1
>
> P40M3M4Het_merged.sorted.filtered.bam 2
>
> P14M3M4Het_merged.sorted.filtered.bam 1
>
>
>
>
> On Wed, Mar 14, 2018 at 11:36 AM, seyfim ***@***.******@***.***><mail
***@***.******@***.***>><mailto:
> ***@***.******@***.******@***.***>>> wrote:
>
> > I have two sets (either P14M3M4 or P40M3M4) and the comparisons for
each
> > set are sample1: Wt, Wt, Mut then sample 2: Mut, Het, Het respectively
> > On Mar 14, 2018, at 12:33 PM, goldenflaw ***@***.******@***.***>
***@***.***><mail
> ***@***.******@***.******@***.***>><mailto:
> > ***@***.******@***.******@***.***><mailto:
***@***.******@***.***>>>> wrote:
> >
> > Thanks, but I'm not sure I understand? Which 3 samples are condition 1
> and
> > which 3 are condition 2?
> > Best,
> > Yang
> >
> > On Wed, Mar 14, 2018 at 11:21 AM, mh406910 ***@***.******@***.***>
***@***.***>
> ***@***.***><
> > ***@***.***>> wrote:
> >
> > > Hello,
> > >
> > > So after reviewing the files I did have the correct samples. The
> > > comparisons are as follows:
> > >
> > >
> > >
> > > P14M3M4Wt_merged.sorted.filtered.bam vs P14M3M4Mut_merged.sorted.
> > > filtered.bam
> > >
> > > P14M3M4Wt_merged.sorted.filtered.bam vs P14M3M4Het_merged.sorted.
> > > filtered.bam
> > >
> > > P14M3M4Mut_merged.sorted.filtered.bam . vs
P14M3M4Het_merged.sorted.
> > > filtered.bam
> > >
> > > P40M3M4Wt_merged.sorted.filtered.bam vs P40M3M4Mut_merged.sorted.
> > > filtered.bam
> > >
> > > P40M3M4Wt_merged.sorted.filtered.bam vs P40M3M4Het_merged.sorted.
> > > filtered.bam
> > >
> > > P40M3M4Mut_merged.sorted.filtered.bam vs P40M3M4Het_merged.sorted.
> > > filtered.bam
> > >
> > >
> > > Thanks,
> > > Marilyn E. Seyfi
> > > Bioinformatics Technologist
> > > Cleveland Clinic Genomic Medicine Institute
> > > work email: ***@***.******@***.******@***.***><mailto:
***@***.******@***.***>><mailto:
> ***@***.******@***.******@***.***>>
> > > mobile: (740)-603-2131 <(740)%20603-2131> <(740)%20603-2131>
<(740)%20603-2131>
> <(740)%20603-2131>
> > >
> > >
> > >
> > >
> > > ________________________________
> > > From: goldenflaw ***@***.******@***.***><mailto:
***@***.******@***.***>><mailto:
> ***@***.******@***.******@***.***>><mailto:
***@***.***
> > com>>
> > > Sent: Tuesday, March 13, 2018 6:35 PM
> > >
> > > To: davidaknowles/leafcutter
> > > Cc: Seyfi, Marilyn; Comment
> > > Subject: Re: [davidaknowles/leafcutter] small sample size affecting
> > > cluster significance detection? (#56)
> > >
> > > These samples are from the leafcutter output that you gave me (
> > > test_perind_numers.counts.gz
> > > <https://github.com/davidaknowles/leafcutter/files/1797264/t
> est_perind_
> > > numers.counts.gz>
> > > )
> > >
> > > On Tue, Mar 13, 2018 at 5:32 PM, mh406910 ***@***.******@***.***>
***@***.***>
> ***@***.***><
> > ***@***.***>>
> > > wrote:
> > >
> > > > Well those are not correct.. It should be P14Wt or P40Wt (sample
1)
> vs
> > > > P14Mut or P40Mut (sample 2)... I included all comparisons in the
> .junc
> > > step
> > > > and the following intro cluster step --was that incorrect?
> > > >
> > > > Get Outlook for Android<https://aka.ms/ghei36>
> > > >
> > > > ________________________________
> > > > From: goldenflaw ***@***.******@***.***><mailto:
***@***.******@***.***>><mailto:
> ***@***.******@***.******@***.***>><mailto:
> > ***@***.******@***.******@***.***><mailto:
***@***.******@***.***>>>>
> > > > Sent: Tuesday, March 13, 2018 6:27:23 PM
> > > >
> > > > To: davidaknowles/leafcutter
> > > > Cc: Seyfi, Marilyn; Comment
> > > > Subject: Re: [davidaknowles/leafcutter] small sample size
affecting
> > > > cluster significance detection? (#56)
> > > >
> > > > I see that you have 6 samples:
> > > >
> > > > P40M3M4Wt_merged.sorted.filtered.bam P14M3M4Mut_merged.sorted.
> > > filtered.bam
> > > > P40M3M4Mut_merged.sorted.filtered.bam P14M3M4Wt_merged.sorted.
> > > filtered.bam
> > > > P40M3M4Het_merged.sorted.filtered.bam P14M3M4Het_merged.sorted.
> > > > filtered.bam
> > > >
> > > >
> > > > Could you tell me which ones are "condition 1" and which ones are
> > > > "condition 2".
> > > >
> > > > On Tue, Mar 13, 2018 at 5:25 PM, mh406910 <
***@***.******@***.******@***.***>
> ***@***.***><
> > ***@***.***>>
> > > > wrote:
> > > >
> > > > > Just to clarify you mean the ban file? As well as the output
from
> > rMATS
> > > > > and MISO with their highest delta pi value for the selected
sample
> > > > > comparison?
> > > > >
> > > > > Get Outlook for Android<https://aka.ms/ghei36>
> > > > >
> > > > > ________________________________
> > > > > From: goldenflaw ***@***.******@***.***><mailto:
***@***.******@***.***>><mailto:
> ***@***.******@***.******@***.***>><mailto:
> > ***@***.******@***.******@***.***><mailto:
***@***.******@***.***>>>>
> > > > > Sent: Tuesday, March 13, 2018 6:23:24 PM
> > > > >
> > > > > To: davidaknowles/leafcutter
> > > > > Cc: Seyfi, Marilyn; Comment
> > > > > Subject: Re: [davidaknowles/leafcutter] small sample size
> affecting
> > > > > cluster significance detection? (#56)
> > > > >
> > > > > Could you provide the correct mapping of samples to conditions?
> And
> > > your
> > > > > strongest "hit" from rMATS and or MISO.
> > > > >
> > > > > Best,
> > > > > Yang
> > > > >
> > > > > On Tue, Mar 13, 2018 at 5:21 PM, mh406910 <
> ***@***.******@***.******@***.***><mailto:
***@***.******@***.***>><
> > ***@***.***>>
> > > > > wrote:
> > > > >
> > > > > > Also when I run your program with the replicates unmerged as
> > separate
> > > > > > replicates I get the same error that there are no significant
> > > clusters.
> > > > > > MISO and rMATS both report otherwise.
> > > > > >
> > > > > > Get Outlook for Android<https://aka.ms/ghei36>
> > > > > >
> > > > > > ________________________________
> > > > > > From: goldenflaw ***@***.******@***.***><mailto:
***@***.******@***.***>><mailto:
> ***@***.******@***.******@***.***>><mailto:
> > ***@***.******@***.******@***.***><mailto:
***@***.******@***.***>>>>
> > > > > > Sent: Tuesday, March 13, 2018 3:02:47 PM
> > > > > > To: davidaknowles/leafcutter
> > > > > > Cc: Seyfi, Marilyn; Comment
> > > > > > Subject: Re: [davidaknowles/leafcutter] small sample size
> > affecting
> > > > > > cluster significance detection? (#56)
> > > > > >
> > > > > > Your P14WTmut.txt file looks wrong, you only have 2 samples in
> > there.
> > > > > >
> > > > > > Best,
> > > > > > Yang
> > > > > >
> > > > > > On Fri, Mar 9, 2018 at 9:07 AM, Yang Li ***@***.******@***.***>
***@***.***>
> ***@***.***>
> > ***@***.***>>
> > > wrote:
> > > > > >
> > > > > > > I will have a look at the whole thing.
> > > > > > >
> > > > > > > Best,
> > > > > > > Yang
> > > > > > >
> > > > > > > On Mar 9, 2018 8:54 AM, "seyfim" ***@***.******@***.***>
***@***.***>
> ***@***.***><
> > ***@***.***>> wrote:
> > > > > > >
> > > > > > >> how do I just share one chromosome with you?
> > > > > > >>
> > > > > > >> —
> > > > > > >> You are receiving this because you were mentioned.
> > > > > > >> Reply to this email directly, view it on GitHub
> > > > > > >> <https://github.com/davidaknowles/leafcutter/
> > > > issues/56#issuecomment-
> > > > > > 371835036>,
> > > > > > >> or mute the thread
> > > > > > >> <https://github.com/notifications/unsubscribe-auth/
> > > > > > AE1piZqBGBpzf2cNNshOQCmtkfMdzzChks5tcpe2gaJpZM4Si2YZ>
> > > > > > >> .
> > > > > > >>
> > > > > > >
> > > > > >
> > > > > > —
> > > > > > You are receiving this because you commented.
> > > > > > Reply to this email directly, view it on GitHub<
> > https://github.com/
> > > > > > davidaknowles/leafcutter#56#issuecomment-372781944>,
or
> > mute
> > > > the
> > > > > > thread<https://github.com/notifications/unsubscribe-auth/
> > > > > > AH0qV7HiNDq4nRYq6MBi9a1xWDnMNfEUks5teBfWgaJpZM4Si2YZ>.
> > > > > >
> > > > > > —
> > > > > > You are receiving this because you were mentioned.
> > > > > > Reply to this email directly, view it on GitHub
> > > > > > <https://github.com/davidaknowles/leafcutter/
> > issues/56#issuecomment-
> > > > > 372838727>,
> > > > > > or mute the thread
> > > > > > <https://github.com/notifications/unsubscribe-auth/AE1pif2tfb_
> > > > > R056uBWbmrOrB1zLXuxdoks5teEZOgaJpZM4Si2YZ>
> > > > > > .
> > > > > >
> > > > >
> > > > > —
> > > > > You are receiving this because you commented.
> > > > > Reply to this email directly, view it on GitHub<
> https://github.com/
> > > > > davidaknowles/leafcutter#56#issuecomment-372839266>, or
> mute
> > > the
> > > > > thread<https://github.com/notifications/unsubscribe-auth/
> > > > > AH0qV4a50BHXeGYRRfHWzlaqB1rvfmN4ks5teEbcgaJpZM4Si2YZ>.
> > > > >
> > > > > —
> > > > > You are receiving this because you were mentioned.
> > > > > Reply to this email directly, view it on GitHub
> > > > > <#56 (comment)
> comment-
> > > > 372839683>,
> > > > > or mute the thread
> > > > > <https://github.com/notifications/unsubscribe-auth/
> > > > AE1piXefiUjlA0HwvzOEvT5OynDQUxMiks5teEdOgaJpZM4Si2YZ>
> > > > > .
> > > > >
> > > >
> > > > —
> > > > You are receiving this because you commented.
> > > > Reply to this email directly, view it on GitHub<
https://github.com/
> > > > davidaknowles/leafcutter#56#issuecomment-372840184>, or
mute
> > the
> > > > thread<https://github.com/notifications/unsubscribe-auth/AH0
qV7Aqc_
> > > > xXMWmaRAqFAffdAH88FYvWks5teEfKgaJpZM4Si2YZ>.
> > > >
> > > > —
> > > > You are receiving this because you were mentioned.
> > > > Reply to this email directly, view it on GitHub
> > > > <#56 (comment)
comment-
> > > 372841413>,
> > > > or mute the thread
> > > > <https://github.com/notifications/unsubscribe-auth/
> > > AE1pifjojIveXOgnlLQb8BSregse9Dcvks5teEkNgaJpZM4Si2YZ>
> > > > .
> > > >
> > >
> > > —
> > > You are receiving this because you commented.
> > > Reply to this email directly, view it on GitHub<https://github.com/
> > > davidaknowles/leafcutter#56#issuecomment-372842066>, or mute
> the
> > > thread<https://github.com/notifications/unsubscribe-auth/
> > > AH0qVyVeY6qZqaqwDsXLAfyjgplfknB6ks5teEmqgaJpZM4Si2YZ>.
> > >
> > > —
> > > You are receiving this because you were mentioned.
> > > Reply to this email directly, view it on GitHub
> > > <#56 (comment)-
> > 373083237>,
> > > or mute the thread
> > > <https://github.com/notifications/unsubscribe-auth/AE1picyeYN0qgm8x_
> > 1MbtBCWV5AT8eLNks5teUNwgaJpZM4Si2YZ>
> > > .
> > >
> >
> > —
> > You are receiving this because you authored the thread.
> > Reply to this email directly, view it on GitHub<https://github.com/
> > davidaknowles/leafcutter#56#issuecomment-373087793>, or mute
the
> > thread<https://github.com/notifications/unsubscribe-
> > auth/AikLJbxBarvHE4PBpQbaL4R-FYiOc51Nks5teUZhgaJpZM4Si2YZ>.
> >
> >
> > ===================================
> >
> >
> > Please consider the environment before printing this e-mail
> >
> > Cleveland Clinic is currently ranked as the No. 2 hospital in the
> country
> > by U.S. News & World Report (2017-2018). Visit us online at
> > http://www.clevelandclinic.org for a complete listing of our
services,
> > staff and locations. Confidentiality Note: This message is intended
for
> use
> > only by the individual or entity to which it is addressed and may
> contain
> > information that is privileged, confidential, and exempt from
disclosure
> > under applicable law. If the reader of this message is not the
intended
> > recipient or the employee or agent responsible for delivering the
> message
> > to the intended recipient, you are hereby notified that any
> dissemination,
> > distribution or copying of this communication is strictly prohibited.
If
> > you have received this communication in error, please contact the
sender
> > immediately and destroy the material in its entirety, whether
electronic
> or
> > hard copy. Thank you.
> >
> > —
> > You are receiving this because you were mentioned.
> > Reply to this email directly, view it on GitHub
> > <#56 (comment)
> comment-373088665>,
> > or mute the thread
> > <https://github.com/notifications/unsubscribe-auth/AE1pidgjz
> q9SV9YW1Is63NaIjtwNSMBOks5teUb2gaJpZM4Si2YZ>
> > .
> >
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub<https://github.com/davi
> daknowles/leafcutter/issues/56#issuecomment-373426027>, or mute the
> thread<https://github.com/notifications/unsubscribe-auth/Aik
> LJUmD86LbwVjw_rwMERYtyO6Bixt0ks5teo6NgaJpZM4Si2YZ>.
>
>
> ===================================
>
>
> Please consider the environment before printing this e-mail
>
> Cleveland Clinic is currently ranked as the No. 2 hospital in the
country
> by U.S. News & World Report (2017-2018). Visit us online at
> http://www.clevelandclinic.org for a complete listing of our services,
> staff and locations. Confidentiality Note: This message is intended for
use
> only by the individual or entity to which it is addressed and may
contain
> information that is privileged, confidential, and exempt from disclosure
> under applicable law. If the reader of this message is not the intended
> recipient or the employee or agent responsible for delivering the
message
> to the intended recipient, you are hereby notified that any
dissemination,
> distribution or copying of this communication is strictly prohibited. If
> you have received this communication in error, please contact the sender
> immediately and destroy the material in its entirety, whether electronic
or
> hard copy. Thank you.
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <#56 (comment)
comment-373445540>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AE1piQRwl
OQtSEbOoIORNeFr0Un8sXFlks5tepuigaJpZM4Si2YZ>
> .
>
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub<https://github.com/davi
daknowles/leafcutter/issues/56#issuecomment-373448275>, or mute the
thread<https://github.com/notifications/unsubscribe-auth/Aik
LJRJjEQjxZtUsXPvFOXwhZhiGL6Imks5tep1ygaJpZM4Si2YZ>.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country
by U.S. News & World Report (2017-2018). Visit us online at
http://www.clevelandclinic.org for a complete listing of our services,
staff and locations. Confidentiality Note: This message is intended for use
only by the individual or entity to which it is addressed and may contain
information that is privileged, confidential, and exempt from disclosure
under applicable law. If the reader of this message is not the intended
recipient or the employee or agent responsible for delivering the message
to the intended recipient, you are hereby notified that any dissemination,
distribution or copying of this communication is strictly prohibited. If
you have received this communication in error, please contact the sender
immediately and destroy the material in its entirety, whether electronic or
hard copy. Thank you.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#56 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AE1piQx0dpuNbNOdXk8aKGXqe3Y7Ltvnks5tep3SgaJpZM4Si2YZ>
.
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub<#56 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AikLJSYz4JVvW-I6fgEs_fjQtl5pM_5Wks5tep6ngaJpZM4Si2YZ>.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
from leafcutter.
goldenflaw
commented on September 19, 2024
Please use the above assignment to rerun leafcutter (with all 6 samples).
Best,
Yang
…On Mar 15, 2018 12:06, "seyfim" ***@***.***> wrote:
I know what that means, I have paired end sequencing reads...
On Mar 15, 2018, at 1:02 PM, goldenflaw ***@***.***<mailto:
***@***.***>> wrote:
"Paired-end" data does not refer to paired samples comparisons, it refers
to paired-end reads. Please have a look at the output files when you do
not
match up your samples for comparisons.
Best,
Yang
On Thu, Mar 15, 2018 at 11:58 AM, seyfim ***@***.***<mailto:
***@***.***>> wrote:
> No, I specifically used commands for paired-end data in both rMATS and
> MISO.
> So, basically I cannot use your tool?
> On Mar 15, 2018, at 12:57 PM, goldenflaw ***@***.***<
***@***.***><mailto:
> ***@***.******@***.***>>> wrote:
>
> LeafCutter (and I believe the other tools that you used) does not
support
> paired samples. When I ran your test without pairing, I get some
> significant hits.
>
> Best,
> Yang
>
> On Thu, Mar 15, 2018 at 11:49 AM, seyfim ***@***.***<
***@***.***><mailto:
> ***@***.******@***.***>>> wrote:
>
> > Sorry for not being clear!
> > Yes those are the 2 classes but within each class I do a comparison
like
> > the following:
> > P14M3M4Wt_merged.sorted.filtered.bam (1) vs
> P14M3M4Mut_merged.sorted.filtered.bam
> > (1)
> > Or
> > P40M3M4Wt_merged.sorted.filtered.bam (2) vs
> P40M3M4Wt_merged.sorted.filtered.bam
> > (2)
> >
> > I make sure to differentiate the different classes with their
> > corresponding comparisons in my test.junc files and in my intron_diff
> files
> >
> > On Mar 15, 2018, at 11:53 AM, goldenflaw ***@***.***<
***@***.***><mail
> ***@***.******@***.***>><mailto:
> > ***@***.******@***.***><mailto:
***@***.***>>> wrote:
> >
> > I'm still confused are the assignments as such:
> >
> > P40M3M4Wt_merged.sorted.filtered.bam 2
> >
> > P14M3M4Mut_merged.sorted.filtered.bam 1
> >
> > P40M3M4Wt_merged.sorted.filtered.bam 2
> >
> > P14M3M4Wt_merged.sorted.filtered.bam 1
> >
> > P40M3M4Het_merged.sorted.filtered.bam 2
> >
> > P14M3M4Het_merged.sorted.filtered.bam 1
> >
> >
> >
> >
> > On Wed, Mar 14, 2018 at 11:36 AM, seyfim ***@***.***<
***@***.***><mail
> ***@***.******@***.***>><mailto:
> > ***@***.******@***.***><mailto:
***@***.***>>> wrote:
> >
> > > I have two sets (either P14M3M4 or P40M3M4) and the comparisons for
> each
> > > set are sample1: Wt, Wt, Mut then sample 2: Mut, Het, Het
respectively
> > > On Mar 14, 2018, at 12:33 PM, goldenflaw ***@***.***<
***@***.***>
> ***@***.***><mail
> > ***@***.******@***.***><mailto:
***@***.***>><mailto:
> > > ***@***.******@***.***><mailto:
***@***.***><mailto:
> ***@***.******@***.***>>>> wrote:
> > >
> > > Thanks, but I'm not sure I understand? Which 3 samples are condition
1
> > and
> > > which 3 are condition 2?
> > > Best,
> > > Yang
> > >
> > > On Wed, Mar 14, 2018 at 11:21 AM, mh406910 ***@***.***
***@***.***>
> ***@***.***>
> > ***@***.***><
> > > ***@***.***>> wrote:
> > >
> > > > Hello,
> > > >
> > > > So after reviewing the files I did have the correct samples. The
> > > > comparisons are as follows:
> > > >
> > > >
> > > >
> > > > P14M3M4Wt_merged.sorted.filtered.bam vs P14M3M4Mut_merged.sorted.
> > > > filtered.bam
> > > >
> > > > P14M3M4Wt_merged.sorted.filtered.bam vs P14M3M4Het_merged.sorted.
> > > > filtered.bam
> > > >
> > > > P14M3M4Mut_merged.sorted.filtered.bam . vs
> P14M3M4Het_merged.sorted.
> > > > filtered.bam
> > > >
> > > > P40M3M4Wt_merged.sorted.filtered.bam vs P40M3M4Mut_merged.sorted.
> > > > filtered.bam
> > > >
> > > > P40M3M4Wt_merged.sorted.filtered.bam vs P40M3M4Het_merged.sorted.
> > > > filtered.bam
> > > >
> > > > P40M3M4Mut_merged.sorted.filtered.bam vs
P40M3M4Het_merged.sorted.
> > > > filtered.bam
> > > >
> > > >
> > > > Thanks,
> > > > Marilyn E. Seyfi
> > > > Bioinformatics Technologist
> > > > Cleveland Clinic Genomic Medicine Institute
> > > > work email: ***@***.******@***.***><mailto:
***@***.***><mailto:
> ***@***.******@***.***>><mailto:
> > ***@***.******@***.******@***.***>>
> > > > mobile: (740)-603-2131 <(740)%20603-2131> <(740)%20603-2131>
<(740)%20603-2131>
> <(740)%20603-2131>
> > <(740)%20603-2131>
> > > >
> > > >
> > > >
> > > >
> > > > ________________________________
> > > > From: goldenflaw ***@***.***<mailto:
***@***.***><mailto:
> ***@***.******@***.***>><mailto:
> > ***@***.******@***.***><mailto:
***@***.***>><mailto:
> ***@***.***
> > > com>>
> > > > Sent: Tuesday, March 13, 2018 6:35 PM
> > > >
> > > > To: davidaknowles/leafcutter
> > > > Cc: Seyfi, Marilyn; Comment
> > > > Subject: Re: [davidaknowles/leafcutter] small sample size
affecting
> > > > cluster significance detection? (#56)
> > > >
> > > > These samples are from the leafcutter output that you gave me (
> > > > test_perind_numers.counts.gz
> > > > <https://github.com/davidaknowles/leafcutter/files/1797264/t
> > est_perind_
> > > > numers.counts.gz>
> > > > )
> > > >
> > > > On Tue, Mar 13, 2018 at 5:32 PM, mh406910 <
***@***.******@***.***>
> ***@***.***>
> > ***@***.***><
> > > ***@***.***>>
> > > > wrote:
> > > >
> > > > > Well those are not correct.. It should be P14Wt or P40Wt (sample
> 1)
> > vs
> > > > > P14Mut or P40Mut (sample 2)... I included all comparisons in the
> > .junc
> > > > step
> > > > > and the following intro cluster step --was that incorrect?
> > > > >
> > > > > Get Outlook for Android<https://aka.ms/ghei36>
> > > > >
> > > > > ________________________________
> > > > > From: goldenflaw ***@***.***<mailto:
***@***.***><mailto:
> ***@***.******@***.***>><mailto:
> > ***@***.******@***.***><mailto:
***@***.***>><mailto:
> > > ***@***.******@***.***><mailto:
***@***.***><mailto:
> ***@***.******@***.***>>>>
> > > > > Sent: Tuesday, March 13, 2018 6:27:23 PM
> > > > >
> > > > > To: davidaknowles/leafcutter
> > > > > Cc: Seyfi, Marilyn; Comment
> > > > > Subject: Re: [davidaknowles/leafcutter] small sample size
> affecting
> > > > > cluster significance detection? (#56)
> > > > >
> > > > > I see that you have 6 samples:
> > > > >
> > > > > P40M3M4Wt_merged.sorted.filtered.bam P14M3M4Mut_merged.sorted.
> > > > filtered.bam
> > > > > P40M3M4Mut_merged.sorted.filtered.bam P14M3M4Wt_merged.sorted.
> > > > filtered.bam
> > > > > P40M3M4Het_merged.sorted.filtered.bam P14M3M4Het_merged.sorted.
> > > > > filtered.bam
> > > > >
> > > > >
> > > > > Could you tell me which ones are "condition 1" and which ones
are
> > > > > "condition 2".
> > > > >
> > > > > On Tue, Mar 13, 2018 at 5:25 PM, mh406910 <
> ***@***.******@***.***><mailto:
***@***.***>
> > ***@***.***><
> > > ***@***.***>>
> > > > > wrote:
> > > > >
> > > > > > Just to clarify you mean the ban file? As well as the output
> from
> > > rMATS
> > > > > > and MISO with their highest delta pi value for the selected
> sample
> > > > > > comparison?
> > > > > >
> > > > > > Get Outlook for Android<https://aka.ms/ghei36>
> > > > > >
> > > > > > ________________________________
> > > > > > From: goldenflaw ***@***.***<mailto:
***@***.***><mailto:
> ***@***.******@***.***>><mailto:
> > ***@***.******@***.***><mailto:
***@***.***>><mailto:
> > > ***@***.******@***.***><mailto:
***@***.***><mailto:
> ***@***.******@***.***>>>>
> > > > > > Sent: Tuesday, March 13, 2018 6:23:24 PM
> > > > > >
> > > > > > To: davidaknowles/leafcutter
> > > > > > Cc: Seyfi, Marilyn; Comment
> > > > > > Subject: Re: [davidaknowles/leafcutter] small sample size
> > affecting
> > > > > > cluster significance detection? (#56)
> > > > > >
> > > > > > Could you provide the correct mapping of samples to
conditions?
> > And
> > > > your
> > > > > > strongest "hit" from rMATS and or MISO.
> > > > > >
> > > > > > Best,
> > > > > > Yang
> > > > > >
> > > > > > On Tue, Mar 13, 2018 at 5:21 PM, mh406910 <
> > ***@***.******@***.***><mailto:
***@***.***><mailto:
> ***@***.******@***.***>><
> > > ***@***.***>>
> > > > > > wrote:
> > > > > >
> > > > > > > Also when I run your program with the replicates unmerged as
> > > separate
> > > > > > > replicates I get the same error that there are no
significant
> > > > clusters.
> > > > > > > MISO and rMATS both report otherwise.
> > > > > > >
> > > > > > > Get Outlook for Android<https://aka.ms/ghei36>
> > > > > > >
> > > > > > > ________________________________
> > > > > > > From: goldenflaw ***@***.***<mailto:
***@***.***><mailto:
> ***@***.******@***.***>><mailto:
> > ***@***.******@***.***><mailto:
***@***.***>><mailto:
> > > ***@***.******@***.***><mailto:
***@***.***><mailto:
> ***@***.******@***.***>>>>
> > > > > > > Sent: Tuesday, March 13, 2018 3:02:47 PM
> > > > > > > To: davidaknowles/leafcutter
> > > > > > > Cc: Seyfi, Marilyn; Comment
> > > > > > > Subject: Re: [davidaknowles/leafcutter] small sample size
> > > affecting
> > > > > > > cluster significance detection? (#56)
> > > > > > >
> > > > > > > Your P14WTmut.txt file looks wrong, you only have 2 samples
in
> > > there.
> > > > > > >
> > > > > > > Best,
> > > > > > > Yang
> > > > > > >
> > > > > > > On Fri, Mar 9, 2018 at 9:07 AM, Yang Li <
***@***.******@***.***>
> ***@***.***>
> > ***@***.***>
> > > ***@***.***>>
> > > > wrote:
> > > > > > >
> > > > > > > > I will have a look at the whole thing.
> > > > > > > >
> > > > > > > > Best,
> > > > > > > > Yang
> > > > > > > >
> > > > > > > > On Mar 9, 2018 8:54 AM, "seyfim" ***@***.***
***@***.***>
> ***@***.***>
> > ***@***.***><
> > > ***@***.***>> wrote:
> > > > > > > >
> > > > > > > >> how do I just share one chromosome with you?
> > > > > > > >>
> > > > > > > >> —
> > > > > > > >> You are receiving this because you were mentioned.
> > > > > > > >> Reply to this email directly, view it on GitHub
> > > > > > > >> <https://github.com/davidaknowles/leafcutter/
> > > > > issues/56#issuecomment-
> > > > > > > 371835036>,
> > > > > > > >> or mute the thread
> > > > > > > >> <https://github.com/notifications/unsubscribe-auth/
> > > > > > > AE1piZqBGBpzf2cNNshOQCmtkfMdzzChks5tcpe2gaJpZM4Si2YZ>
> > > > > > > >> .
> > > > > > > >>
> > > > > > > >
> > > > > > >
> > > > > > > —
> > > > > > > You are receiving this because you commented.
> > > > > > > Reply to this email directly, view it on GitHub<
> > > https://github.com/
> > > > > > > davidaknowles/leafcutter#56#issuecomment-372781944>,
> or
> > > mute
> > > > > the
> > > > > > > thread<https://github.com/notifications/unsubscribe-auth/
> > > > > > > AH0qV7HiNDq4nRYq6MBi9a1xWDnMNfEUks5teBfWgaJpZM4Si2YZ>.
> > > > > > >
> > > > > > > —
> > > > > > > You are receiving this because you were mentioned.
> > > > > > > Reply to this email directly, view it on GitHub
> > > > > > > <https://github.com/davidaknowles/leafcutter/
> > > issues/56#issuecomment-
> > > > > > 372838727>,
> > > > > > > or mute the thread
> > > > > > > <https://github.com/notifications/unsubscribe-
auth/AE1pif2tfb_
> > > > > > R056uBWbmrOrB1zLXuxdoks5teEZOgaJpZM4Si2YZ>
> > > > > > > .
> > > > > > >
> > > > > >
> > > > > > —
> > > > > > You are receiving this because you commented.
> > > > > > Reply to this email directly, view it on GitHub<
> > https://github.com/
> > > > > > davidaknowles/leafcutter#56#issuecomment-372839266>,
or
> > mute
> > > > the
> > > > > > thread<https://github.com/notifications/unsubscribe-auth/
> > > > > > AH0qV4a50BHXeGYRRfHWzlaqB1rvfmN4ks5teEbcgaJpZM4Si2YZ>.
> > > > > >
> > > > > > —
> > > > > > You are receiving this because you were mentioned.
> > > > > > Reply to this email directly, view it on GitHub
> > > > > > <#56 (comment)
> > comment-
> > > > > 372839683>,
> > > > > > or mute the thread
> > > > > > <https://github.com/notifications/unsubscribe-auth/
> > > > > AE1piXefiUjlA0HwvzOEvT5OynDQUxMiks5teEdOgaJpZM4Si2YZ>
> > > > > > .
> > > > > >
> > > > >
> > > > > —
> > > > > You are receiving this because you commented.
> > > > > Reply to this email directly, view it on GitHub<
> https://github.com/
> > > > > davidaknowles/leafcutter#56#issuecomment-372840184>, or
> mute
> > > the
> > > > > thread<https://github.com/notifications/unsubscribe-auth/AH0
> qV7Aqc_
> > > > > xXMWmaRAqFAffdAH88FYvWks5teEfKgaJpZM4Si2YZ>.
> > > > >
> > > > > —
> > > > > You are receiving this because you were mentioned.
> > > > > Reply to this email directly, view it on GitHub
> > > > > <#56 (comment)
> comment-
> > > > 372841413>,
> > > > > or mute the thread
> > > > > <https://github.com/notifications/unsubscribe-auth/
> > > > AE1pifjojIveXOgnlLQb8BSregse9Dcvks5teEkNgaJpZM4Si2YZ>
> > > > > .
> > > > >
> > > >
> > > > —
> > > > You are receiving this because you commented.
> > > > Reply to this email directly, view it on GitHub<
https://github.com/
> > > > davidaknowles/leafcutter#56#issuecomment-372842066>, or
mute
> > the
> > > > thread<https://github.com/notifications/unsubscribe-auth/
> > > > AH0qVyVeY6qZqaqwDsXLAfyjgplfknB6ks5teEmqgaJpZM4Si2YZ>.
> > > >
> > > > —
> > > > You are receiving this because you were mentioned.
> > > > Reply to this email directly, view it on GitHub
> > > > <https://github.com/davidaknowles/leafcutter/
issues/56#issuecomment-
> > > 373083237>,
> > > > or mute the thread
> > > > <https://github.com/notifications/unsubscribe-
auth/AE1picyeYN0qgm8x_
> > > 1MbtBCWV5AT8eLNks5teUNwgaJpZM4Si2YZ>
> > > > .
> > > >
> > >
> > > —
> > > You are receiving this because you authored the thread.
> > > Reply to this email directly, view it on GitHub<https://github.com/
> > > davidaknowles/leafcutter#56#issuecomment-373087793>, or mute
> the
> > > thread<https://github.com/notifications/unsubscribe-
> > > auth/AikLJbxBarvHE4PBpQbaL4R-FYiOc51Nks5teUZhgaJpZM4Si2YZ>.
> > >
> > >
> > > ===================================
> > >
> > >
> > > Please consider the environment before printing this e-mail
> > >
> > > Cleveland Clinic is currently ranked as the No. 2 hospital in the
> > country
> > > by U.S. News & World Report (2017-2018). Visit us online at
> > > http://www.clevelandclinic.org for a complete listing of our
> services,
> > > staff and locations. Confidentiality Note: This message is intended
> for
> > use
> > > only by the individual or entity to which it is addressed and may
> > contain
> > > information that is privileged, confidential, and exempt from
> disclosure
> > > under applicable law. If the reader of this message is not the
> intended
> > > recipient or the employee or agent responsible for delivering the
> > message
> > > to the intended recipient, you are hereby notified that any
> > dissemination,
> > > distribution or copying of this communication is strictly
prohibited.
> If
> > > you have received this communication in error, please contact the
> sender
> > > immediately and destroy the material in its entirety, whether
> electronic
> > or
> > > hard copy. Thank you.
> > >
> > > —
> > > You are receiving this because you were mentioned.
> > > Reply to this email directly, view it on GitHub
> > > <#56 (comment)
> > comment-373088665>,
> > > or mute the thread
> > > <https://github.com/notifications/unsubscribe-auth/AE1pidgjz
> > q9SV9YW1Is63NaIjtwNSMBOks5teUb2gaJpZM4Si2YZ>
> > > .
> > >
> >
> > —
> > You are receiving this because you authored the thread.
> > Reply to this email directly, view it on GitHub<
https://github.com/davi
> > daknowles/leafcutter/issues/56#issuecomment-373426027>, or mute the
> > thread<https://github.com/notifications/unsubscribe-auth/Aik
> > LJUmD86LbwVjw_rwMERYtyO6Bixt0ks5teo6NgaJpZM4Si2YZ>.
> >
> >
> > ===================================
> >
> >
> > Please consider the environment before printing this e-mail
> >
> > Cleveland Clinic is currently ranked as the No. 2 hospital in the
> country
> > by U.S. News & World Report (2017-2018). Visit us online at
> > http://www.clevelandclinic.org for a complete listing of our
services,
> > staff and locations. Confidentiality Note: This message is intended
for
> use
> > only by the individual or entity to which it is addressed and may
> contain
> > information that is privileged, confidential, and exempt from
disclosure
> > under applicable law. If the reader of this message is not the
intended
> > recipient or the employee or agent responsible for delivering the
> message
> > to the intended recipient, you are hereby notified that any
> dissemination,
> > distribution or copying of this communication is strictly prohibited.
If
> > you have received this communication in error, please contact the
sender
> > immediately and destroy the material in its entirety, whether
electronic
> or
> > hard copy. Thank you.
> >
> > —
> > You are receiving this because you were mentioned.
> > Reply to this email directly, view it on GitHub
> > <#56 (comment)
> comment-373445540>,
> > or mute the thread
> > <https://github.com/notifications/unsubscribe-auth/AE1piQRwl
> OQtSEbOoIORNeFr0Un8sXFlks5tepuigaJpZM4Si2YZ>
> > .
> >
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub<https://github.com/davi
> daknowles/leafcutter/issues/56#issuecomment-373448275>, or mute the
> thread<https://github.com/notifications/unsubscribe-auth/Aik
> LJRJjEQjxZtUsXPvFOXwhZhiGL6Imks5tep1ygaJpZM4Si2YZ>.
>
>
> ===================================
>
>
> Please consider the environment before printing this e-mail
>
> Cleveland Clinic is currently ranked as the No. 2 hospital in the
country
> by U.S. News & World Report (2017-2018). Visit us online at
> http://www.clevelandclinic.org for a complete listing of our services,
> staff and locations. Confidentiality Note: This message is intended for
use
> only by the individual or entity to which it is addressed and may
contain
> information that is privileged, confidential, and exempt from disclosure
> under applicable law. If the reader of this message is not the intended
> recipient or the employee or agent responsible for delivering the
message
> to the intended recipient, you are hereby notified that any
dissemination,
> distribution or copying of this communication is strictly prohibited. If
> you have received this communication in error, please contact the sender
> immediately and destroy the material in its entirety, whether electronic
or
> hard copy. Thank you.
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <#56 (comment)-
373448797>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/
AE1piQx0dpuNbNOdXk8aKGXqe3Y7Ltvnks5tep3SgaJpZM4Si2YZ>
> .
>
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub<https://github.com/
davidaknowles/leafcutter#56#issuecomment-373450060>, or mute the
thread<https://github.com/notifications/unsubscribe-
auth/AikLJSYz4JVvW-I6fgEs_fjQtl5pM_5Wks5tep6ngaJpZM4Si2YZ>.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country
by U.S. News & World Report (2017-2018). Visit us online at
http://www.clevelandclinic.org for a complete listing of our services,
staff and locations. Confidentiality Note: This message is intended for use
only by the individual or entity to which it is addressed and may contain
information that is privileged, confidential, and exempt from disclosure
under applicable law. If the reader of this message is not the intended
recipient or the employee or agent responsible for delivering the message
to the intended recipient, you are hereby notified that any dissemination,
distribution or copying of this communication is strictly prohibited. If
you have received this communication in error, please contact the sender
immediately and destroy the material in its entirety, whether electronic or
hard copy. Thank you.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#56 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AE1piYvjK7I4AcqI3_fVzNZxQ9Nm8sRrks5tep-wgaJpZM4Si2YZ>
.
from leafcutter.
seyfim
commented on September 19, 2024
Then what am I testing for? The comparison is the whole point of the analysis. Could you please explain what you mean?
On Mar 15, 2018, at 1:17 PM, goldenflaw <[email protected]<mailto:[email protected]>> wrote:
Please use the above assignment to rerun leafcutter (with all 6 samples).
Best,
Yang
On Mar 15, 2018 12:06, "seyfim" ***@***.******@***.***>> wrote:
I know what that means, I have paired end sequencing reads...
On Mar 15, 2018, at 1:02 PM, goldenflaw ***@***.******@***.***><mailto:
***@***.******@***.***>>> wrote:
"Paired-end" data does not refer to paired samples comparisons, it refers
to paired-end reads. Please have a look at the output files when you do
not
match up your samples for comparisons.
Best,
Yang
On Thu, Mar 15, 2018 at 11:58 AM, seyfim ***@***.******@***.***><mailto:
***@***.******@***.***>>> wrote:
> No, I specifically used commands for paired-end data in both rMATS and
> MISO.
> So, basically I cannot use your tool?
> On Mar 15, 2018, at 12:57 PM, goldenflaw ***@***.******@***.***><
***@***.***><mailto:
> ***@***.******@***.******@***.***>>> wrote:
>
> LeafCutter (and I believe the other tools that you used) does not
support
> paired samples. When I ran your test without pairing, I get some
> significant hits.
>
> Best,
> Yang
>
> On Thu, Mar 15, 2018 at 11:49 AM, seyfim ***@***.******@***.***><
***@***.***><mailto:
> ***@***.******@***.******@***.***>>> wrote:
>
> > Sorry for not being clear!
> > Yes those are the 2 classes but within each class I do a comparison
like
> > the following:
> > P14M3M4Wt_merged.sorted.filtered.bam (1) vs
> P14M3M4Mut_merged.sorted.filtered.bam
> > (1)
> > Or
> > P40M3M4Wt_merged.sorted.filtered.bam (2) vs
> P40M3M4Wt_merged.sorted.filtered.bam
> > (2)
> >
> > I make sure to differentiate the different classes with their
> > corresponding comparisons in my test.junc files and in my intron_diff
> files
> >
> > On Mar 15, 2018, at 11:53 AM, goldenflaw ***@***.******@***.***><
***@***.***><mail
> ***@***.******@***.******@***.***>><mailto:
> > ***@***.******@***.******@***.***><mailto:
***@***.******@***.***>>>> wrote:
> >
> > I'm still confused are the assignments as such:
> >
> > P40M3M4Wt_merged.sorted.filtered.bam 2
> >
> > P14M3M4Mut_merged.sorted.filtered.bam 1
> >
> > P40M3M4Wt_merged.sorted.filtered.bam 2
> >
> > P14M3M4Wt_merged.sorted.filtered.bam 1
> >
> > P40M3M4Het_merged.sorted.filtered.bam 2
> >
> > P14M3M4Het_merged.sorted.filtered.bam 1
> >
> >
> >
> >
> > On Wed, Mar 14, 2018 at 11:36 AM, seyfim ***@***.******@***.***><
***@***.***><mail
> ***@***.******@***.******@***.***>><mailto:
> > ***@***.******@***.******@***.***><mailto:
***@***.******@***.***>>>> wrote:
> >
> > > I have two sets (either P14M3M4 or P40M3M4) and the comparisons for
> each
> > > set are sample1: Wt, Wt, Mut then sample 2: Mut, Het, Het
respectively
> > > On Mar 14, 2018, at 12:33 PM, goldenflaw ***@***.******@***.***><
***@***.***>
> ***@***.***><mail
> > ***@***.******@***.******@***.***><mailto:
***@***.******@***.***>>><mailto:
> > > ***@***.******@***.******@***.***><mailto:
***@***.******@***.***>><mailto:
> ***@***.******@***.******@***.***>>>> wrote:
> > >
> > > Thanks, but I'm not sure I understand? Which 3 samples are condition
1
> > and
> > > which 3 are condition 2?
> > > Best,
> > > Yang
> > >
> > > On Wed, Mar 14, 2018 at 11:21 AM, mh406910 ***@***.******@***.***>
***@***.***>
> ***@***.***>
> > ***@***.***><
> > > ***@***.***>> wrote:
> > >
> > > > Hello,
> > > >
> > > > So after reviewing the files I did have the correct samples. The
> > > > comparisons are as follows:
> > > >
> > > >
> > > >
> > > > P14M3M4Wt_merged.sorted.filtered.bam vs P14M3M4Mut_merged.sorted.
> > > > filtered.bam
> > > >
> > > > P14M3M4Wt_merged.sorted.filtered.bam vs P14M3M4Het_merged.sorted.
> > > > filtered.bam
> > > >
> > > > P14M3M4Mut_merged.sorted.filtered.bam . vs
> P14M3M4Het_merged.sorted.
> > > > filtered.bam
> > > >
> > > > P40M3M4Wt_merged.sorted.filtered.bam vs P40M3M4Mut_merged.sorted.
> > > > filtered.bam
> > > >
> > > > P40M3M4Wt_merged.sorted.filtered.bam vs P40M3M4Het_merged.sorted.
> > > > filtered.bam
> > > >
> > > > P40M3M4Mut_merged.sorted.filtered.bam vs
P40M3M4Het_merged.sorted.
> > > > filtered.bam
> > > >
> > > >
> > > > Thanks,
> > > > Marilyn E. Seyfi
> > > > Bioinformatics Technologist
> > > > Cleveland Clinic Genomic Medicine Institute
> > > > work email: ***@***.******@***.******@***.***><mailto:
***@***.******@***.***>><mailto:
> ***@***.******@***.******@***.***>><mailto:
> > ***@***.******@***.******@***.******@***.***>>
> > > > mobile: (740)-603-2131 <(740)%20603-2131> <(740)%20603-2131>
<(740)%20603-2131>
> <(740)%20603-2131>
> > <(740)%20603-2131>
> > > >
> > > >
> > > >
> > > >
> > > > ________________________________
> > > > From: goldenflaw ***@***.******@***.***><mailto:
***@***.******@***.***>><mailto:
> ***@***.******@***.******@***.***>><mailto:
> > ***@***.******@***.******@***.***><mailto:
***@***.******@***.***>>><mailto:
> ***@***.***
> > > com>>
> > > > Sent: Tuesday, March 13, 2018 6:35 PM
> > > >
> > > > To: davidaknowles/leafcutter
> > > > Cc: Seyfi, Marilyn; Comment
> > > > Subject: Re: [davidaknowles/leafcutter] small sample size
affecting
> > > > cluster significance detection? (#56)
> > > >
> > > > These samples are from the leafcutter output that you gave me (
> > > > test_perind_numers.counts.gz
> > > > <https://github.com/davidaknowles/leafcutter/files/1797264/t
> > est_perind_
> > > > numers.counts.gz>
> > > > )
> > > >
> > > > On Tue, Mar 13, 2018 at 5:32 PM, mh406910 <
***@***.******@***.******@***.***>
> ***@***.***>
> > ***@***.***><
> > > ***@***.***>>
> > > > wrote:
> > > >
> > > > > Well those are not correct.. It should be P14Wt or P40Wt (sample
> 1)
> > vs
> > > > > P14Mut or P40Mut (sample 2)... I included all comparisons in the
> > .junc
> > > > step
> > > > > and the following intro cluster step --was that incorrect?
> > > > >
> > > > > Get Outlook for Android<https://aka.ms/ghei36>
> > > > >
> > > > > ________________________________
> > > > > From: goldenflaw ***@***.******@***.***><mailto:
***@***.******@***.***>><mailto:
> ***@***.******@***.******@***.***>><mailto:
> > ***@***.******@***.******@***.***><mailto:
***@***.******@***.***>>><mailto:
> > > ***@***.******@***.******@***.***><mailto:
***@***.******@***.***>><mailto:
> ***@***.******@***.******@***.***>>>>
> > > > > Sent: Tuesday, March 13, 2018 6:27:23 PM
> > > > >
> > > > > To: davidaknowles/leafcutter
> > > > > Cc: Seyfi, Marilyn; Comment
> > > > > Subject: Re: [davidaknowles/leafcutter] small sample size
> affecting
> > > > > cluster significance detection? (#56)
> > > > >
> > > > > I see that you have 6 samples:
> > > > >
> > > > > P40M3M4Wt_merged.sorted.filtered.bam P14M3M4Mut_merged.sorted.
> > > > filtered.bam
> > > > > P40M3M4Mut_merged.sorted.filtered.bam P14M3M4Wt_merged.sorted.
> > > > filtered.bam
> > > > > P40M3M4Het_merged.sorted.filtered.bam P14M3M4Het_merged.sorted.
> > > > > filtered.bam
> > > > >
> > > > >
> > > > > Could you tell me which ones are "condition 1" and which ones
are
> > > > > "condition 2".
> > > > >
> > > > > On Tue, Mar 13, 2018 at 5:25 PM, mh406910 <
> ***@***.******@***.******@***.***><mailto:
***@***.******@***.***>>
> > ***@***.***><
> > > ***@***.***>>
> > > > > wrote:
> > > > >
> > > > > > Just to clarify you mean the ban file? As well as the output
> from
> > > rMATS
> > > > > > and MISO with their highest delta pi value for the selected
> sample
> > > > > > comparison?
> > > > > >
> > > > > > Get Outlook for Android<https://aka.ms/ghei36>
> > > > > >
> > > > > > ________________________________
> > > > > > From: goldenflaw ***@***.******@***.***><mailto:
***@***.******@***.***>><mailto:
> ***@***.******@***.******@***.***>><mailto:
> > ***@***.******@***.******@***.***><mailto:
***@***.******@***.***>>><mailto:
> > > ***@***.******@***.******@***.***><mailto:
***@***.******@***.***>><mailto:
> ***@***.******@***.******@***.***>>>>
> > > > > > Sent: Tuesday, March 13, 2018 6:23:24 PM
> > > > > >
> > > > > > To: davidaknowles/leafcutter
> > > > > > Cc: Seyfi, Marilyn; Comment
> > > > > > Subject: Re: [davidaknowles/leafcutter] small sample size
> > affecting
> > > > > > cluster significance detection? (#56)
> > > > > >
> > > > > > Could you provide the correct mapping of samples to
conditions?
> > And
> > > > your
> > > > > > strongest "hit" from rMATS and or MISO.
> > > > > >
> > > > > > Best,
> > > > > > Yang
> > > > > >
> > > > > > On Tue, Mar 13, 2018 at 5:21 PM, mh406910 <
> > ***@***.******@***.******@***.***><mailto:
***@***.******@***.***>><mailto:
> ***@***.******@***.******@***.***>><
> > > ***@***.***>>
> > > > > > wrote:
> > > > > >
> > > > > > > Also when I run your program with the replicates unmerged as
> > > separate
> > > > > > > replicates I get the same error that there are no
significant
> > > > clusters.
> > > > > > > MISO and rMATS both report otherwise.
> > > > > > >
> > > > > > > Get Outlook for Android<https://aka.ms/ghei36>
> > > > > > >
> > > > > > > ________________________________
> > > > > > > From: goldenflaw ***@***.******@***.***><mailto:
***@***.******@***.***>><mailto:
> ***@***.******@***.******@***.***>><mailto:
> > ***@***.******@***.******@***.***><mailto:
***@***.******@***.***>>><mailto:
> > > ***@***.******@***.******@***.***><mailto:
***@***.******@***.***>><mailto:
> ***@***.******@***.******@***.***>>>>
> > > > > > > Sent: Tuesday, March 13, 2018 3:02:47 PM
> > > > > > > To: davidaknowles/leafcutter
> > > > > > > Cc: Seyfi, Marilyn; Comment
> > > > > > > Subject: Re: [davidaknowles/leafcutter] small sample size
> > > affecting
> > > > > > > cluster significance detection? (#56)
> > > > > > >
> > > > > > > Your P14WTmut.txt file looks wrong, you only have 2 samples
in
> > > there.
> > > > > > >
> > > > > > > Best,
> > > > > > > Yang
> > > > > > >
> > > > > > > On Fri, Mar 9, 2018 at 9:07 AM, Yang Li <
***@***.******@***.******@***.***>
> ***@***.***>
> > ***@***.***>
> > > ***@***.***>>
> > > > wrote:
> > > > > > >
> > > > > > > > I will have a look at the whole thing.
> > > > > > > >
> > > > > > > > Best,
> > > > > > > > Yang
> > > > > > > >
> > > > > > > > On Mar 9, 2018 8:54 AM, "seyfim" ***@***.******@***.***>
***@***.***>
> ***@***.***>
> > ***@***.***><
> > > ***@***.***>> wrote:
> > > > > > > >
> > > > > > > >> how do I just share one chromosome with you?
> > > > > > > >>
> > > > > > > >> —
> > > > > > > >> You are receiving this because you were mentioned.
> > > > > > > >> Reply to this email directly, view it on GitHub
> > > > > > > >> <https://github.com/davidaknowles/leafcutter/
> > > > > issues/56#issuecomment-
> > > > > > > 371835036>,
> > > > > > > >> or mute the thread
> > > > > > > >> <https://github.com/notifications/unsubscribe-auth/
> > > > > > > AE1piZqBGBpzf2cNNshOQCmtkfMdzzChks5tcpe2gaJpZM4Si2YZ>
> > > > > > > >> .
> > > > > > > >>
> > > > > > > >
> > > > > > >
> > > > > > > —
> > > > > > > You are receiving this because you commented.
> > > > > > > Reply to this email directly, view it on GitHub<
> > > https://github.com/
> > > > > > > davidaknowles/leafcutter#56#issuecomment-372781944>,
> or
> > > mute
> > > > > the
> > > > > > > thread<https://github.com/notifications/unsubscribe-auth/
> > > > > > > AH0qV7HiNDq4nRYq6MBi9a1xWDnMNfEUks5teBfWgaJpZM4Si2YZ>.
> > > > > > >
> > > > > > > —
> > > > > > > You are receiving this because you were mentioned.
> > > > > > > Reply to this email directly, view it on GitHub
> > > > > > > <https://github.com/davidaknowles/leafcutter/
> > > issues/56#issuecomment-
> > > > > > 372838727>,
> > > > > > > or mute the thread
> > > > > > > <https://github.com/notifications/unsubscribe-
auth/AE1pif2tfb_
> > > > > > R056uBWbmrOrB1zLXuxdoks5teEZOgaJpZM4Si2YZ>
> > > > > > > .
> > > > > > >
> > > > > >
> > > > > > —
> > > > > > You are receiving this because you commented.
> > > > > > Reply to this email directly, view it on GitHub<
> > https://github.com/
> > > > > > davidaknowles/leafcutter#56#issuecomment-372839266>,
or
> > mute
> > > > the
> > > > > > thread<https://github.com/notifications/unsubscribe-auth/
> > > > > > AH0qV4a50BHXeGYRRfHWzlaqB1rvfmN4ks5teEbcgaJpZM4Si2YZ>.
> > > > > >
> > > > > > —
> > > > > > You are receiving this because you were mentioned.
> > > > > > Reply to this email directly, view it on GitHub
> > > > > > <#56 (comment)
> > comment-
> > > > > 372839683>,
> > > > > > or mute the thread
> > > > > > <https://github.com/notifications/unsubscribe-auth/
> > > > > AE1piXefiUjlA0HwvzOEvT5OynDQUxMiks5teEdOgaJpZM4Si2YZ>
> > > > > > .
> > > > > >
> > > > >
> > > > > —
> > > > > You are receiving this because you commented.
> > > > > Reply to this email directly, view it on GitHub<
> https://github.com/
> > > > > davidaknowles/leafcutter#56#issuecomment-372840184>, or
> mute
> > > the
> > > > > thread<https://github.com/notifications/unsubscribe-auth/AH0
> qV7Aqc_
> > > > > xXMWmaRAqFAffdAH88FYvWks5teEfKgaJpZM4Si2YZ>.
> > > > >
> > > > > —
> > > > > You are receiving this because you were mentioned.
> > > > > Reply to this email directly, view it on GitHub
> > > > > <#56 (comment)
> comment-
> > > > 372841413>,
> > > > > or mute the thread
> > > > > <https://github.com/notifications/unsubscribe-auth/
> > > > AE1pifjojIveXOgnlLQb8BSregse9Dcvks5teEkNgaJpZM4Si2YZ>
> > > > > .
> > > > >
> > > >
> > > > —
> > > > You are receiving this because you commented.
> > > > Reply to this email directly, view it on GitHub<
https://github.com/
> > > > davidaknowles/leafcutter#56#issuecomment-372842066>, or
mute
> > the
> > > > thread<https://github.com/notifications/unsubscribe-auth/
> > > > AH0qVyVeY6qZqaqwDsXLAfyjgplfknB6ks5teEmqgaJpZM4Si2YZ>.
> > > >
> > > > —
> > > > You are receiving this because you were mentioned.
> > > > Reply to this email directly, view it on GitHub
> > > > <https://github.com/davidaknowles/leafcutter/
issues/56#issuecomment-
> > > 373083237>,
> > > > or mute the thread
> > > > <https://github.com/notifications/unsubscribe-
auth/AE1picyeYN0qgm8x_
> > > 1MbtBCWV5AT8eLNks5teUNwgaJpZM4Si2YZ>
> > > > .
> > > >
> > >
> > > —
> > > You are receiving this because you authored the thread.
> > > Reply to this email directly, view it on GitHub<https://github.com/
> > > davidaknowles/leafcutter#56#issuecomment-373087793>, or mute
> the
> > > thread<https://github.com/notifications/unsubscribe-
> > > auth/AikLJbxBarvHE4PBpQbaL4R-FYiOc51Nks5teUZhgaJpZM4Si2YZ>.
> > >
> > >
> > > ===================================
> > >
> > >
> > > Please consider the environment before printing this e-mail
> > >
> > > Cleveland Clinic is currently ranked as the No. 2 hospital in the
> > country
> > > by U.S. News & World Report (2017-2018). Visit us online at
> > > http://www.clevelandclinic.org for a complete listing of our
> services,
> > > staff and locations. Confidentiality Note: This message is intended
> for
> > use
> > > only by the individual or entity to which it is addressed and may
> > contain
> > > information that is privileged, confidential, and exempt from
> disclosure
> > > under applicable law. If the reader of this message is not the
> intended
> > > recipient or the employee or agent responsible for delivering the
> > message
> > > to the intended recipient, you are hereby notified that any
> > dissemination,
> > > distribution or copying of this communication is strictly
prohibited.
> If
> > > you have received this communication in error, please contact the
> sender
> > > immediately and destroy the material in its entirety, whether
> electronic
> > or
> > > hard copy. Thank you.
> > >
> > > —
> > > You are receiving this because you were mentioned.
> > > Reply to this email directly, view it on GitHub
> > > <#56 (comment)
> > comment-373088665>,
> > > or mute the thread
> > > <https://github.com/notifications/unsubscribe-auth/AE1pidgjz
> > q9SV9YW1Is63NaIjtwNSMBOks5teUb2gaJpZM4Si2YZ>
> > > .
> > >
> >
> > —
> > You are receiving this because you authored the thread.
> > Reply to this email directly, view it on GitHub<
https://github.com/davi
> > daknowles/leafcutter/issues/56#issuecomment-373426027>, or mute the
> > thread<https://github.com/notifications/unsubscribe-auth/Aik
> > LJUmD86LbwVjw_rwMERYtyO6Bixt0ks5teo6NgaJpZM4Si2YZ>.
> >
> >
> > ===================================
> >
> >
> > Please consider the environment before printing this e-mail
> >
> > Cleveland Clinic is currently ranked as the No. 2 hospital in the
> country
> > by U.S. News & World Report (2017-2018). Visit us online at
> > http://www.clevelandclinic.org for a complete listing of our
services,
> > staff and locations. Confidentiality Note: This message is intended
for
> use
> > only by the individual or entity to which it is addressed and may
> contain
> > information that is privileged, confidential, and exempt from
disclosure
> > under applicable law. If the reader of this message is not the
intended
> > recipient or the employee or agent responsible for delivering the
> message
> > to the intended recipient, you are hereby notified that any
> dissemination,
> > distribution or copying of this communication is strictly prohibited.
If
> > you have received this communication in error, please contact the
sender
> > immediately and destroy the material in its entirety, whether
electronic
> or
> > hard copy. Thank you.
> >
> > —
> > You are receiving this because you were mentioned.
> > Reply to this email directly, view it on GitHub
> > <#56 (comment)
> comment-373445540>,
> > or mute the thread
> > <https://github.com/notifications/unsubscribe-auth/AE1piQRwl
> OQtSEbOoIORNeFr0Un8sXFlks5tepuigaJpZM4Si2YZ>
> > .
> >
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub<https://github.com/davi
> daknowles/leafcutter/issues/56#issuecomment-373448275>, or mute the
> thread<https://github.com/notifications/unsubscribe-auth/Aik
> LJRJjEQjxZtUsXPvFOXwhZhiGL6Imks5tep1ygaJpZM4Si2YZ>.
>
>
> ===================================
>
>
> Please consider the environment before printing this e-mail
>
> Cleveland Clinic is currently ranked as the No. 2 hospital in the
country
> by U.S. News & World Report (2017-2018). Visit us online at
> http://www.clevelandclinic.org for a complete listing of our services,
> staff and locations. Confidentiality Note: This message is intended for
use
> only by the individual or entity to which it is addressed and may
contain
> information that is privileged, confidential, and exempt from disclosure
> under applicable law. If the reader of this message is not the intended
> recipient or the employee or agent responsible for delivering the
message
> to the intended recipient, you are hereby notified that any
dissemination,
> distribution or copying of this communication is strictly prohibited. If
> you have received this communication in error, please contact the sender
> immediately and destroy the material in its entirety, whether electronic
or
> hard copy. Thank you.
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <#56 (comment)-
373448797>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/
AE1piQx0dpuNbNOdXk8aKGXqe3Y7Ltvnks5tep3SgaJpZM4Si2YZ>
> .
>
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub<https://github.com/
davidaknowles/leafcutter#56#issuecomment-373450060>, or mute the
thread<https://github.com/notifications/unsubscribe-
auth/AikLJSYz4JVvW-I6fgEs_fjQtl5pM_5Wks5tep6ngaJpZM4Si2YZ>.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country
by U.S. News & World Report (2017-2018). Visit us online at
http://www.clevelandclinic.org for a complete listing of our services,
staff and locations. Confidentiality Note: This message is intended for use
only by the individual or entity to which it is addressed and may contain
information that is privileged, confidential, and exempt from disclosure
under applicable law. If the reader of this message is not the intended
recipient or the employee or agent responsible for delivering the message
to the intended recipient, you are hereby notified that any dissemination,
distribution or copying of this communication is strictly prohibited. If
you have received this communication in error, please contact the sender
immediately and destroy the material in its entirety, whether electronic or
hard copy. Thank you.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#56 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AE1piYvjK7I4AcqI3_fVzNZxQ9Nm8sRrks5tep-wgaJpZM4Si2YZ>
.
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub<#56 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AikLJcUcmEfIPtEzddd2abZTNUtzgNQYks5teqIXgaJpZM4Si2YZ>.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
from leafcutter.
goldenflaw
commented on September 19, 2024
You are testing differences in splicing between two conditions, if you do
not have at least 2 samples per condition, you cannot use LeafCutter.
On Mar 15, 2018 12:20, "seyfim" <[email protected]> wrote:
Then what am I testing for? The comparison is the whole point of the
analysis. Could you please explain what you mean?
On Mar 15, 2018, at 1:17 PM, goldenflaw <[email protected]<mailto:
[email protected]>> wrote:
Please use the above assignment to rerun leafcutter (with all 6 samples).
Best,
Yang
On Mar 15, 2018 12:06, "seyfim" <[email protected]<mailto:
[email protected]>> wrote:
I know what that means, I have paired end sequencing reads...
On Mar 15, 2018, at 1:02 PM, goldenflaw ***@***.***<mailto:
[email protected]><mailto:
***@***.******@***.***>>> wrote:
"Paired-end" data does not refer to paired samples comparisons, it refers
to paired-end reads. Please have a look at the output files when you do
not
match up your samples for comparisons.
Best,
Yang
On Thu, Mar 15, 2018 at 11:58 AM, seyfim ***@***.***<mailto:
[email protected]><mailto:
***@***.******@***.***>>> wrote:
> No, I specifically used commands for paired-end data in both rMATS and
> MISO.
> So, basically I cannot use your tool?
> On Mar 15, 2018, at 12:57 PM, goldenflaw ***@***.***<
mailto:[email protected]><
***@***.***><mailto:
> ***@***.******@***.***><mailto:
[email protected]>>> wrote:
>
> LeafCutter (and I believe the other tools that you used) does not
support
> paired samples. When I ran your test without pairing, I get some
> significant hits.
>
> Best,
> Yang
>
> On Thu, Mar 15, 2018 at 11:49 AM, seyfim ***@***.***<
mailto:[email protected]><
***@***.***><mailto:
> ***@***.******@***.***><mailto:
[email protected]>>> wrote:
>
> > Sorry for not being clear!
> > Yes those are the 2 classes but within each class I do a comparison
like
> > the following:
> > P14M3M4Wt_merged.sorted.filtered.bam (1) vs
> P14M3M4Mut_merged.sorted.filtered.bam
> > (1)
> > Or
> > P40M3M4Wt_merged.sorted.filtered.bam (2) vs
> P40M3M4Wt_merged.sorted.filtered.bam
> > (2)
> >
> > I make sure to differentiate the different classes with their
> > corresponding comparisons in my test.junc files and in my intron_diff
> files
> >
> > On Mar 15, 2018, at 11:53 AM, goldenflaw ***@***.***<
mailto:[email protected]><
***@***.***><mail
> ***@***.******@***.***><mailto:
[email protected]>><mailto:
> > ***@***.******@***.***><mailto:
[email protected]><mailto:
***@***.******@***.***>>>> wrote:
> >
> > I'm still confused are the assignments as such:
> >
> > P40M3M4Wt_merged.sorted.filtered.bam 2
> >
> > P14M3M4Mut_merged.sorted.filtered.bam 1
> >
> > P40M3M4Wt_merged.sorted.filtered.bam 2
> >
> > P14M3M4Wt_merged.sorted.filtered.bam 1
> >
> > P40M3M4Het_merged.sorted.filtered.bam 2
> >
> > P14M3M4Het_merged.sorted.filtered.bam 1
> >
> >
> >
> >
> > On Wed, Mar 14, 2018 at 11:36 AM, seyfim ***@***.***<
mailto:[email protected]><
***@***.***><mail
> ***@***.******@***.***><mailto:
[email protected]>><mailto:
> > ***@***.******@***.***><mailto:
[email protected]><mailto:
***@***.******@***.***>>>> wrote:
> >
> > > I have two sets (either P14M3M4 or P40M3M4) and the comparisons for
> each
> > > set are sample1: Wt, Wt, Mut then sample 2: Mut, Het, Het
respectively
> > > On Mar 14, 2018, at 12:33 PM, goldenflaw ***@***.***<
mailto:[email protected]><
***@***.***>
> ***@***.***><mail
> > ***@***.******@***.***><mailto:
[email protected]><mailto:
***@***.******@***.***>>><mailto:
> > > ***@***.******@***.***><mailto:
[email protected]><mailto:
***@***.******@***.***>><mailto:
> ***@***.******@***.***><mailto:
[email protected]>>>> wrote:
> > >
> > > Thanks, but I'm not sure I understand? Which 3 samples are
condition
1
> > and
> > > which 3 are condition 2?
> > > Best,
> > > Yang
> > >
> > > On Wed, Mar 14, 2018 at 11:21 AM, mh406910 ***@***.***
<mailto:[email protected]>
***@***.***>
> ***@***.***>
> > ***@***.***><
> > > ***@***.***>> wrote:
> > >
> > > > Hello,
> > > >
> > > > So after reviewing the files I did have the correct samples. The
> > > > comparisons are as follows:
> > > >
> > > >
> > > >
> > > > P14M3M4Wt_merged.sorted.filtered.bam vs P14M3M4Mut_merged.sorted.
> > > > filtered.bam
> > > >
> > > > P14M3M4Wt_merged.sorted.filtered.bam vs P14M3M4Het_merged.sorted.
> > > > filtered.bam
> > > >
> > > > P14M3M4Mut_merged.sorted.filtered.bam . vs
> P14M3M4Het_merged.sorted.
> > > > filtered.bam
> > > >
> > > > P40M3M4Wt_merged.sorted.filtered.bam vs P40M3M4Mut_merged.sorted.
> > > > filtered.bam
> > > >
> > > > P40M3M4Wt_merged.sorted.filtered.bam vs P40M3M4Het_merged.sorted.
> > > > filtered.bam
> > > >
> > > > P40M3M4Mut_merged.sorted.filtered.bam vs
P40M3M4Het_merged.sorted.
> > > > filtered.bam
> > > >
> > > >
> > > > Thanks,
> > > > Marilyn E. Seyfi
> > > > Bioinformatics Technologist
> > > > Cleveland Clinic Genomic Medicine Institute
> > > > work email: ***@***.******@***.***><mailto:
[email protected]><mailto:
***@***.******@***.***>><mailto:
> ***@***.******@***.******@***.***>><mailto:
> > ***@***.******@***.******@***.***><mailto:
> > > > mobile: (740)-603-2131 <(740)%20603-2131> <(740)%20603-2131>
<(740)%20603-2131>
<(740)%20603-2131>
> <(740)%20603-2131>
> > <(740)%20603-2131>
> > > >
> > > >
> > > >
> > > >
> > > > ________________________________
> > > > From: goldenflaw ***@***.***<mailto:
[email protected]><mailto:
***@***.******@***.***>><mailto:
> ***@***.******@***.***><mailto:
[email protected]>><mailto:
> > ***@***.******@***.***><mailto:
[email protected]><mailto:
***@***.******@***.***>>><mailto:
> ***@***.***
> > > com>>
> > > > Sent: Tuesday, March 13, 2018 6:35 PM
> > > >
> > > > To: davidaknowles/leafcutter
> > > > Cc: Seyfi, Marilyn; Comment
> > > > Subject: Re: [davidaknowles/leafcutter] small sample size
affecting
> > > > cluster significance detection? (#56)
> > > >
> > > > These samples are from the leafcutter output that you gave me (
> > > > test_perind_numers.counts.gz
> > > > <https://github.com/davidaknowles/leafcutter/files/1797264/t
> > est_perind_
> > > > numers.counts.gz>
> > > > )
> > > >
> > > > On Tue, Mar 13, 2018 at 5:32 PM, mh406910 <
***@***.******@***.***><mailto:
> ***@***.***>
> > ***@***.***><
> > > ***@***.***>>
> > > > wrote:
> > > >
> > > > > Well those are not correct.. It should be P14Wt or P40Wt
(sample
> 1)
> > vs
> > > > > P14Mut or P40Mut (sample 2)... I included all comparisons in
the
> > .junc
> > > > step
> > > > > and the following intro cluster step --was that incorrect?
> > > > >
> > > > > Get Outlook for Android<https://aka.ms/ghei36>
> > > > >
> > > > > ________________________________
> > > > > From: goldenflaw ***@***.***<mailto:
[email protected]><mailto:
***@***.******@***.***>><mailto:
> ***@***.******@***.***><mailto:
[email protected]>><mailto:
> > ***@***.******@***.***><mailto:
[email protected]><mailto:
***@***.******@***.***>>><mailto:
> > > ***@***.******@***.***><mailto:
[email protected]><mailto:
***@***.******@***.***>><mailto:
> ***@***.******@***.***><mailto:
> > > > > Sent: Tuesday, March 13, 2018 6:27:23 PM
> > > > >
> > > > > To: davidaknowles/leafcutter
> > > > > Cc: Seyfi, Marilyn; Comment
> > > > > Subject: Re: [davidaknowles/leafcutter] small sample size
> affecting
> > > > > cluster significance detection? (#56)
> > > > >
> > > > > I see that you have 6 samples:
> > > > >
> > > > > P40M3M4Wt_merged.sorted.filtered.bam P14M3M4Mut_merged.sorted.
> > > > filtered.bam
> > > > > P40M3M4Mut_merged.sorted.filtered.bam P14M3M4Wt_merged.sorted.
> > > > filtered.bam
> > > > > P40M3M4Het_merged.sorted.filtered.bam P14M3M4Het_merged.sorted.
> > > > > filtered.bam
> > > > >
> > > > >
> > > > > Could you tell me which ones are "condition 1" and which ones
are
> > > > > "condition 2".
> > > > >
> > > > > On Tue, Mar 13, 2018 at 5:25 PM, mh406910 <
> ***@***.******@***.***><mailto:
[email protected]><mailto:
***@***.******@***.***>>
> > ***@***.***><
> > > ***@***.***>>
> > > > > wrote:
> > > > >
> > > > > > Just to clarify you mean the ban file? As well as the output
> from
> > > rMATS
> > > > > > and MISO with their highest delta pi value for the selected
> sample
> > > > > > comparison?
> > > > > >
> > > > > > Get Outlook for Android<https://aka.ms/ghei36>
> > > > > >
> > > > > > ________________________________
> > > > > > From: goldenflaw ***@***.***<mailto:
[email protected]><mailto:
***@***.******@***.***>><mailto:
> ***@***.******@***.***><mailto:
[email protected]>><mailto:
> > ***@***.******@***.***><mailto:
[email protected]><mailto:
***@***.******@***.***>>><mailto:
> > > ***@***.******@***.***><mailto:
[email protected]><mailto:
***@***.******@***.***>><mailto:
> ***@***.******@***.***><mailto:
> > > > > > Sent: Tuesday, March 13, 2018 6:23:24 PM
> > > > > >
> > > > > > To: davidaknowles/leafcutter
> > > > > > Cc: Seyfi, Marilyn; Comment
> > > > > > Subject: Re: [davidaknowles/leafcutter] small sample size
> > affecting
> > > > > > cluster significance detection? (#56)
> > > > > >
> > > > > > Could you provide the correct mapping of samples to
conditions?
> > And
> > > > your
> > > > > > strongest "hit" from rMATS and or MISO.
> > > > > >
> > > > > > Best,
> > > > > > Yang
> > > > > >
> > > > > > On Tue, Mar 13, 2018 at 5:21 PM, mh406910 <
> > ***@***.******@***.***><mailto:
[email protected]><mailto:
***@***.******@***.***>><mailto:
> ***@***.******@***.***><mailto:
> > > ***@***.***>>
> > > > > > wrote:
> > > > > >
> > > > > > > Also when I run your program with the replicates unmerged
as
> > > separate
> > > > > > > replicates I get the same error that there are no
significant
> > > > clusters.
> > > > > > > MISO and rMATS both report otherwise.
> > > > > > >
> > > > > > > Get Outlook for Android<https://aka.ms/ghei36>
> > > > > > >
> > > > > > > ________________________________
> > > > > > > From: goldenflaw ***@***.***<mailto:
[email protected]><mailto:
***@***.******@***.***>><mailto:
> ***@***.******@***.***><mailto:
[email protected]>><mailto:
> > ***@***.******@***.***><mailto:
[email protected]><mailto:
***@***.******@***.***>>><mailto:
> > > ***@***.******@***.***><mailto:
[email protected]><mailto:
***@***.******@***.***>><mailto:
> ***@***.******@***.***><mailto:
> > > > > > > Sent: Tuesday, March 13, 2018 3:02:47 PM
> > > > > > > To: davidaknowles/leafcutter
> > > > > > > Cc: Seyfi, Marilyn; Comment
> > > > > > > Subject: Re: [davidaknowles/leafcutter] small sample size
> > > affecting
> > > > > > > cluster significance detection? (#56)
> > > > > > >
> > > > > > > Your P14WTmut.txt file looks wrong, you only have 2 samples
in
> > > there.
> > > > > > >
> > > > > > > Best,
> > > > > > > Yang
> > > > > > >
> > > > > > > On Fri, Mar 9, 2018 at 9:07 AM, Yang Li <
***@***.******@***.***><mailto:gol
> ***@***.***>
> > ***@***.***>
> > > ***@***.***>>
> > > > wrote:
> > > > > > >
> > > > > > > > I will have a look at the whole thing.
> > > > > > > >
> > > > > > > > Best,
> > > > > > > > Yang
> > > > > > > >
> > > > > > > > On Mar 9, 2018 8:54 AM, "seyfim" ***@***.***
<mailto:[email protected]>
***@***.***>
> ***@***.***>
> > ***@***.***><
> > > ***@***.***>> wrote:
> > > > > > > >
> > > > > > > >> how do I just share one chromosome with you?
> > > > > > > >>
> > > > > > > >> —
> > > > > > > >> You are receiving this because you were mentioned.
> > > > > > > >> Reply to this email directly, view it on GitHub
> > > > > > > >> <https://github.com/davidaknowles/leafcutter/
> > > > > issues/56#issuecomment-
> > > > > > > 371835036>,
> > > > > > > >> or mute the thread
> > > > > > > >> <https://github.com/notifications/unsubscribe-auth/
> > > > > > > AE1piZqBGBpzf2cNNshOQCmtkfMdzzChks5tcpe2gaJpZM4Si2YZ>
> > > > > > > >> .
> > > > > > > >>
> > > > > > > >
> > > > > > >
> > > > > > > —
> > > > > > > You are receiving this because you commented.
> > > > > > > Reply to this email directly, view it on GitHub<
> > > https://github.com/
> > > > > > > davidaknowles/leafcutter#56#issuecomment-372781944>,
> or
> > > mute
> > > > > the
> > > > > > > thread<https://github.com/notifications/unsubscribe-auth/
> > > > > > > AH0qV7HiNDq4nRYq6MBi9a1xWDnMNfEUks5teBfWgaJpZM4Si2YZ>.
> > > > > > >
> > > > > > > —
> > > > > > > You are receiving this because you were mentioned.
> > > > > > > Reply to this email directly, view it on GitHub
> > > > > > > <https://github.com/davidaknowles/leafcutter/
> > > issues/56#issuecomment-
> > > > > > 372838727>,
> > > > > > > or mute the thread
> > > > > > > <https://github.com/notifications/unsubscribe-
auth/AE1pif2tfb_
> > > > > > R056uBWbmrOrB1zLXuxdoks5teEZOgaJpZM4Si2YZ>
> > > > > > > .
> > > > > > >
> > > > > >
> > > > > > —
> > > > > > You are receiving this because you commented.
> > > > > > Reply to this email directly, view it on GitHub<
> > https://github.com/
> > > > > > davidaknowles/leafcutter#56#issuecomment-372839266>,
or
> > mute
> > > > the
> > > > > > thread<https://github.com/notifications/unsubscribe-auth/
> > > > > > AH0qV4a50BHXeGYRRfHWzlaqB1rvfmN4ks5teEbcgaJpZM4Si2YZ>.
> > > > > >
> > > > > > —
> > > > > > You are receiving this because you were mentioned.
> > > > > > Reply to this email directly, view it on GitHub
> > > > > > <#56 (comment)
> > comment-
> > > > > 372839683>,
> > > > > > or mute the thread
> > > > > > <https://github.com/notifications/unsubscribe-auth/
> > > > > AE1piXefiUjlA0HwvzOEvT5OynDQUxMiks5teEdOgaJpZM4Si2YZ>
> > > > > > .
> > > > > >
> > > > >
> > > > > —
> > > > > You are receiving this because you commented.
> > > > > Reply to this email directly, view it on GitHub<
> https://github.com/
> > > > > davidaknowles/leafcutter#56#issuecomment-372840184>, or
> mute
> > > the
> > > > > thread<https://github.com/notifications/unsubscribe-auth/AH0
> qV7Aqc_
> > > > > xXMWmaRAqFAffdAH88FYvWks5teEfKgaJpZM4Si2YZ>.
> > > > >
> > > > > —
> > > > > You are receiving this because you were mentioned.
> > > > > Reply to this email directly, view it on GitHub
> > > > > <#56 (comment)
> comment-
> > > > 372841413>,
> > > > > or mute the thread
> > > > > <https://github.com/notifications/unsubscribe-auth/
> > > > AE1pifjojIveXOgnlLQb8BSregse9Dcvks5teEkNgaJpZM4Si2YZ>
> > > > > .
> > > > >
> > > >
> > > > —
> > > > You are receiving this because you commented.
> > > > Reply to this email directly, view it on GitHub<
https://github.com/
> > > > davidaknowles/leafcutter#56#issuecomment-372842066>, or
mute
> > the
> > > > thread<https://github.com/notifications/unsubscribe-auth/
> > > > AH0qVyVeY6qZqaqwDsXLAfyjgplfknB6ks5teEmqgaJpZM4Si2YZ>.
> > > >
> > > > —
> > > > You are receiving this because you were mentioned.
> > > > Reply to this email directly, view it on GitHub
> > > > <https://github.com/davidaknowles/leafcutter/
issues/56#issuecomment-
> > > 373083237>,
> > > > or mute the thread
> > > > <https://github.com/notifications/unsubscribe-
auth/AE1picyeYN0qgm8x_
> > > 1MbtBCWV5AT8eLNks5teUNwgaJpZM4Si2YZ>
> > > > .
> > > >
> > >
> > > —
> > > You are receiving this because you authored the thread.
> > > Reply to this email directly, view it on GitHub<https://github.com/
> > > davidaknowles/leafcutter#56#issuecomment-373087793>, or mute
> the
> > > thread<https://github.com/notifications/unsubscribe-
> > > auth/AikLJbxBarvHE4PBpQbaL4R-FYiOc51Nks5teUZhgaJpZM4Si2YZ>.
> > >
> > >
> > > ===================================
> > >
> > >
> > > Please consider the environment before printing this e-mail
> > >
> > > Cleveland Clinic is currently ranked as the No. 2 hospital in the
> > country
> > > by U.S. News & World Report (2017-2018). Visit us online at
> > > http://www.clevelandclinic.org for a complete listing of our
> services,
> > > staff and locations. Confidentiality Note: This message is intended
> for
> > use
> > > only by the individual or entity to which it is addressed and may
> > contain
> > > information that is privileged, confidential, and exempt from
> disclosure
> > > under applicable law. If the reader of this message is not the
> intended
> > > recipient or the employee or agent responsible for delivering the
> > message
> > > to the intended recipient, you are hereby notified that any
> > dissemination,
> > > distribution or copying of this communication is strictly
prohibited.
> If
> > > you have received this communication in error, please contact the
> sender
> > > immediately and destroy the material in its entirety, whether
> electronic
> > or
> > > hard copy. Thank you.
> > >
> > > —
> > > You are receiving this because you were mentioned.
> > > Reply to this email directly, view it on GitHub
> > > <#56 (comment)
> > comment-373088665>,
> > > or mute the thread
> > > <https://github.com/notifications/unsubscribe-auth/AE1pidgjz
> > q9SV9YW1Is63NaIjtwNSMBOks5teUb2gaJpZM4Si2YZ>
> > > .
> > >
> >
> > —
> > You are receiving this because you authored the thread.
> > Reply to this email directly, view it on GitHub<
https://github.com/davi
> > daknowles/leafcutter/issues/56#issuecomment-373426027>, or mute the
> > thread<https://github.com/notifications/unsubscribe-auth/Aik
> > LJUmD86LbwVjw_rwMERYtyO6Bixt0ks5teo6NgaJpZM4Si2YZ>.
> >
> >
> > ===================================
> >
> >
> > Please consider the environment before printing this e-mail
> >
> > Cleveland Clinic is currently ranked as the No. 2 hospital in the
> country
> > by U.S. News & World Report (2017-2018). Visit us online at
> > http://www.clevelandclinic.org for a complete listing of our
services,
> > staff and locations. Confidentiality Note: This message is intended
for
> use
> > only by the individual or entity to which it is addressed and may
> contain
> > information that is privileged, confidential, and exempt from
disclosure
> > under applicable law. If the reader of this message is not the
intended
> > recipient or the employee or agent responsible for delivering the
> message
> > to the intended recipient, you are hereby notified that any
> dissemination,
> > distribution or copying of this communication is strictly prohibited.
If
> > you have received this communication in error, please contact the
sender
> > immediately and destroy the material in its entirety, whether
electronic
> or
> > hard copy. Thank you.
> >
> > —
> > You are receiving this because you were mentioned.
> > Reply to this email directly, view it on GitHub
> > <#56 (comment)
> comment-373445540>,
> > or mute the thread
> > <https://github.com/notifications/unsubscribe-auth/AE1piQRwl
> OQtSEbOoIORNeFr0Un8sXFlks5tepuigaJpZM4Si2YZ>
> > .
> >
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub<https://github.com/davi
> daknowles/leafcutter/issues/56#issuecomment-373448275>, or mute the
> thread<https://github.com/notifications/unsubscribe-auth/Aik
> LJRJjEQjxZtUsXPvFOXwhZhiGL6Imks5tep1ygaJpZM4Si2YZ>.
>
>
> ===================================
>
>
> Please consider the environment before printing this e-mail
>
> Cleveland Clinic is currently ranked as the No. 2 hospital in the
country
> by U.S. News & World Report (2017-2018). Visit us online at
> http://www.clevelandclinic.org for a complete listing of our services,
> staff and locations. Confidentiality Note: This message is intended for
use
> only by the individual or entity to which it is addressed and may
contain
> information that is privileged, confidential, and exempt from
disclosure
> under applicable law. If the reader of this message is not the intended
> recipient or the employee or agent responsible for delivering the
message
> to the intended recipient, you are hereby notified that any
dissemination,
> distribution or copying of this communication is strictly prohibited.
If
> you have received this communication in error, please contact the
sender
> immediately and destroy the material in its entirety, whether
electronic
or
> hard copy. Thank you.
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <#56 (comment)-
373448797>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/
AE1piQx0dpuNbNOdXk8aKGXqe3Y7Ltvnks5tep3SgaJpZM4Si2YZ>
> .
>
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub<https://github.com/
davidaknowles/leafcutter#56#issuecomment-373450060>, or mute the
thread<https://github.com/notifications/unsubscribe-
auth/AikLJSYz4JVvW-I6fgEs_fjQtl5pM_5Wks5tep6ngaJpZM4Si2YZ>.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country
by U.S. News & World Report (2017-2018). Visit us online at
http://www.clevelandclinic.org for a complete listing of our services,
staff and locations. Confidentiality Note: This message is intended for
use
only by the individual or entity to which it is addressed and may contain
information that is privileged, confidential, and exempt from disclosure
under applicable law. If the reader of this message is not the intended
recipient or the employee or agent responsible for delivering the message
to the intended recipient, you are hereby notified that any
dissemination,
distribution or copying of this communication is strictly prohibited. If
you have received this communication in error, please contact the sender
immediately and destroy the material in its entirety, whether electronic
or
hard copy. Thank you.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#56 (comment)-
373451522>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AE1piYvjK7I4AcqI3_
fVzNZxQ9Nm8sRrks5tep-wgaJpZM4Si2YZ>
.
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub<https://github.com/
davidaknowles/leafcutter#56#issuecomment-373454962>, or mute the
thread<https://github.com/notifications/unsubscribe-auth/
AikLJcUcmEfIPtEzddd2abZTNUtzgNQYks5teqIXgaJpZM4Si2YZ>.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country
by U.S. News & World Report (2017-2018). Visit us online at
http://www.clevelandclinic.org for a complete listing of our services,
staff and locations. Confidentiality Note: This message is intended for use
only by the individual or entity to which it is addressed and may contain
information that is privileged, confidential, and exempt from disclosure
under applicable law. If the reader of this message is not the intended
recipient or the employee or agent responsible for delivering the message
to the intended recipient, you are hereby notified that any dissemination,
distribution or copying of this communication is strictly prohibited. If
you have received this communication in error, please contact the sender
immediately and destroy the material in its entirety, whether electronic or
hard copy. Thank you.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#56 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AE1piSVaFzXFuQToZisfk5vtuhahb6dHks5teqLRgaJpZM4Si2YZ>
.
from leafcutter.
seyfim
commented on September 19, 2024
But I did run leafcutter with the unmerged replicate bam files and I still was not generating significance. So this is due to my data being paired-end reads?
On Mar 15, 2018, at 1:25 PM, goldenflaw <[email protected]<mailto:[email protected]>> wrote:
You are testing differences in splicing between two conditions, if you do
not have at least 2 samples per condition, you cannot use LeafCutter.
On Mar 15, 2018 12:20, "seyfim" <[email protected]<mailto:[email protected]>> wrote:
Then what am I testing for? The comparison is the whole point of the
analysis. Could you please explain what you mean?
On Mar 15, 2018, at 1:17 PM, goldenflaw <[email protected]<mailto:[email protected]><mailto:
[email protected]<mailto:[email protected]>>> wrote:
Please use the above assignment to rerun leafcutter (with all 6 samples).
Best,
Yang
On Mar 15, 2018 12:06, "seyfim" <[email protected]<mailto:[email protected]><mailto:
[email protected]<mailto:[email protected]>>> wrote:
I know what that means, I have paired end sequencing reads...
On Mar 15, 2018, at 1:02 PM, goldenflaw ***@***.******@***.***><mailto:
[email protected]<mailto:[email protected]>><mailto:
***@***.******@***.******@***.***>>> wrote:
"Paired-end" data does not refer to paired samples comparisons, it refers
to paired-end reads. Please have a look at the output files when you do
not
match up your samples for comparisons.
Best,
Yang
On Thu, Mar 15, 2018 at 11:58 AM, seyfim ***@***.******@***.***><mailto:
[email protected]<mailto:[email protected]>><mailto:
***@***.******@***.******@***.***>>> wrote:
> No, I specifically used commands for paired-end data in both rMATS and
> MISO.
> So, basically I cannot use your tool?
> On Mar 15, 2018, at 12:57 PM, goldenflaw ***@***.******@***.***><
mailto:[email protected]><
***@***.***><mailto:
> ***@***.******@***.******@***.***><mailto:
[email protected]<mailto:[email protected]>>>> wrote:
>
> LeafCutter (and I believe the other tools that you used) does not
support
> paired samples. When I ran your test without pairing, I get some
> significant hits.
>
> Best,
> Yang
>
> On Thu, Mar 15, 2018 at 11:49 AM, seyfim ***@***.******@***.***><
mailto:[email protected]><
***@***.***><mailto:
> ***@***.******@***.******@***.***><mailto:
[email protected]<mailto:[email protected]>>>> wrote:
>
> > Sorry for not being clear!
> > Yes those are the 2 classes but within each class I do a comparison
like
> > the following:
> > P14M3M4Wt_merged.sorted.filtered.bam (1) vs
> P14M3M4Mut_merged.sorted.filtered.bam
> > (1)
> > Or
> > P40M3M4Wt_merged.sorted.filtered.bam (2) vs
> P40M3M4Wt_merged.sorted.filtered.bam
> > (2)
> >
> > I make sure to differentiate the different classes with their
> > corresponding comparisons in my test.junc files and in my intron_diff
> files
> >
> > On Mar 15, 2018, at 11:53 AM, goldenflaw ***@***.******@***.***><
mailto:[email protected]><
***@***.***><mail
> ***@***.******@***.******@***.***><mailto:
[email protected]<mailto:[email protected]>>><mailto:
> > ***@***.******@***.******@***.***><mailto:
[email protected]<mailto:[email protected]>><mailto:
***@***.******@***.******@***.***>>>> wrote:
> >
> > I'm still confused are the assignments as such:
> >
> > P40M3M4Wt_merged.sorted.filtered.bam 2
> >
> > P14M3M4Mut_merged.sorted.filtered.bam 1
> >
> > P40M3M4Wt_merged.sorted.filtered.bam 2
> >
> > P14M3M4Wt_merged.sorted.filtered.bam 1
> >
> > P40M3M4Het_merged.sorted.filtered.bam 2
> >
> > P14M3M4Het_merged.sorted.filtered.bam 1
> >
> >
> >
> >
> > On Wed, Mar 14, 2018 at 11:36 AM, seyfim ***@***.******@***.***><
mailto:[email protected]><
***@***.***><mail
> ***@***.******@***.******@***.***><mailto:
[email protected]<mailto:[email protected]>>><mailto:
> > ***@***.******@***.******@***.***><mailto:
[email protected]<mailto:[email protected]>><mailto:
***@***.******@***.******@***.***>>>> wrote:
> >
> > > I have two sets (either P14M3M4 or P40M3M4) and the comparisons for
> each
> > > set are sample1: Wt, Wt, Mut then sample 2: Mut, Het, Het
respectively
> > > On Mar 14, 2018, at 12:33 PM, goldenflaw ***@***.******@***.***><
mailto:[email protected]><
***@***.***>
> ***@***.***><mail
> > ***@***.******@***.******@***.***><mailto:
[email protected]<mailto:[email protected]>><mailto:
***@***.******@***.******@***.***>>><mailto:
> > > ***@***.******@***.******@***.***><mailto:
[email protected]<mailto:[email protected]>><mailto:
***@***.******@***.******@***.***>><mailto:
> ***@***.******@***.******@***.***><mailto:
[email protected]<mailto:[email protected]>>>>> wrote:
> > >
> > > Thanks, but I'm not sure I understand? Which 3 samples are
condition
1
> > and
> > > which 3 are condition 2?
> > > Best,
> > > Yang
> > >
> > > On Wed, Mar 14, 2018 at 11:21 AM, mh406910 ***@***.******@***.***>
<mailto:[email protected]>
***@***.***>
> ***@***.***>
> > ***@***.***><
> > > ***@***.***>> wrote:
> > >
> > > > Hello,
> > > >
> > > > So after reviewing the files I did have the correct samples. The
> > > > comparisons are as follows:
> > > >
> > > >
> > > >
> > > > P14M3M4Wt_merged.sorted.filtered.bam vs P14M3M4Mut_merged.sorted.
> > > > filtered.bam
> > > >
> > > > P14M3M4Wt_merged.sorted.filtered.bam vs P14M3M4Het_merged.sorted.
> > > > filtered.bam
> > > >
> > > > P14M3M4Mut_merged.sorted.filtered.bam . vs
> P14M3M4Het_merged.sorted.
> > > > filtered.bam
> > > >
> > > > P40M3M4Wt_merged.sorted.filtered.bam vs P40M3M4Mut_merged.sorted.
> > > > filtered.bam
> > > >
> > > > P40M3M4Wt_merged.sorted.filtered.bam vs P40M3M4Het_merged.sorted.
> > > > filtered.bam
> > > >
> > > > P40M3M4Mut_merged.sorted.filtered.bam vs
P40M3M4Het_merged.sorted.
> > > > filtered.bam
> > > >
> > > >
> > > > Thanks,
> > > > Marilyn E. Seyfi
> > > > Bioinformatics Technologist
> > > > Cleveland Clinic Genomic Medicine Institute
> > > > work email: ***@***.******@***.******@***.***><mailto:
[email protected]<mailto:[email protected]>><mailto:
***@***.******@***.******@***.***>><mailto:
> ***@***.******@***.******@***.******@***.***>><mailto:
> > ***@***.******@***.******@***.******@***.***><mailto:
[email protected]<mailto:[email protected]>>>
> > > > mobile: (740)-603-2131 <(740)%20603-2131> <(740)%20603-2131>
<(740)%20603-2131>
<(740)%20603-2131>
> <(740)%20603-2131>
> > <(740)%20603-2131>
> > > >
> > > >
> > > >
> > > >
> > > > ________________________________
> > > > From: goldenflaw ***@***.******@***.***><mailto:
[email protected]<mailto:[email protected]>><mailto:
***@***.******@***.******@***.***>><mailto:
> ***@***.******@***.******@***.***><mailto:
[email protected]<mailto:[email protected]>>><mailto:
> > ***@***.******@***.******@***.***><mailto:
[email protected]<mailto:[email protected]>><mailto:
***@***.******@***.******@***.***>>><mailto:
> ***@***.***
> > > com>>
> > > > Sent: Tuesday, March 13, 2018 6:35 PM
> > > >
> > > > To: davidaknowles/leafcutter
> > > > Cc: Seyfi, Marilyn; Comment
> > > > Subject: Re: [davidaknowles/leafcutter] small sample size
affecting
> > > > cluster significance detection? (#56)
> > > >
> > > > These samples are from the leafcutter output that you gave me (
> > > > test_perind_numers.counts.gz
> > > > <https://github.com/davidaknowles/leafcutter/files/1797264/t
> > est_perind_
> > > > numers.counts.gz>
> > > > )
> > > >
> > > > On Tue, Mar 13, 2018 at 5:32 PM, mh406910 <
***@***.******@***.******@***.***><mailto:
[email protected]<mailto:[email protected]>>
> ***@***.***>
> > ***@***.***><
> > > ***@***.***>>
> > > > wrote:
> > > >
> > > > > Well those are not correct.. It should be P14Wt or P40Wt
(sample
> 1)
> > vs
> > > > > P14Mut or P40Mut (sample 2)... I included all comparisons in
the
> > .junc
> > > > step
> > > > > and the following intro cluster step --was that incorrect?
> > > > >
> > > > > Get Outlook for Android<https://aka.ms/ghei36>
> > > > >
> > > > > ________________________________
> > > > > From: goldenflaw ***@***.******@***.***><mailto:
[email protected]<mailto:[email protected]>><mailto:
***@***.******@***.******@***.***>><mailto:
> ***@***.******@***.******@***.***><mailto:
[email protected]<mailto:[email protected]>>><mailto:
> > ***@***.******@***.******@***.***><mailto:
[email protected]<mailto:[email protected]>><mailto:
***@***.******@***.******@***.***>>><mailto:
> > > ***@***.******@***.******@***.***><mailto:
[email protected]<mailto:[email protected]>><mailto:
***@***.******@***.******@***.***>><mailto:
> ***@***.******@***.******@***.***><mailto:
[email protected]<mailto:[email protected]>>>>>
> > > > > Sent: Tuesday, March 13, 2018 6:27:23 PM
> > > > >
> > > > > To: davidaknowles/leafcutter
> > > > > Cc: Seyfi, Marilyn; Comment
> > > > > Subject: Re: [davidaknowles/leafcutter] small sample size
> affecting
> > > > > cluster significance detection? (#56)
> > > > >
> > > > > I see that you have 6 samples:
> > > > >
> > > > > P40M3M4Wt_merged.sorted.filtered.bam P14M3M4Mut_merged.sorted.
> > > > filtered.bam
> > > > > P40M3M4Mut_merged.sorted.filtered.bam P14M3M4Wt_merged.sorted.
> > > > filtered.bam
> > > > > P40M3M4Het_merged.sorted.filtered.bam P14M3M4Het_merged.sorted.
> > > > > filtered.bam
> > > > >
> > > > >
> > > > > Could you tell me which ones are "condition 1" and which ones
are
> > > > > "condition 2".
> > > > >
> > > > > On Tue, Mar 13, 2018 at 5:25 PM, mh406910 <
> ***@***.******@***.******@***.***><mailto:
[email protected]<mailto:[email protected]>><mailto:
***@***.******@***.******@***.***>>
> > ***@***.***><
> > > ***@***.***>>
> > > > > wrote:
> > > > >
> > > > > > Just to clarify you mean the ban file? As well as the output
> from
> > > rMATS
> > > > > > and MISO with their highest delta pi value for the selected
> sample
> > > > > > comparison?
> > > > > >
> > > > > > Get Outlook for Android<https://aka.ms/ghei36>
> > > > > >
> > > > > > ________________________________
> > > > > > From: goldenflaw ***@***.******@***.***><mailto:
[email protected]<mailto:[email protected]>><mailto:
***@***.******@***.******@***.***>><mailto:
> ***@***.******@***.******@***.***><mailto:
[email protected]<mailto:[email protected]>>><mailto:
> > ***@***.******@***.******@***.***><mailto:
[email protected]<mailto:[email protected]>><mailto:
***@***.******@***.******@***.***>>><mailto:
> > > ***@***.******@***.******@***.***><mailto:
[email protected]<mailto:[email protected]>><mailto:
***@***.******@***.******@***.***>><mailto:
> ***@***.******@***.******@***.***><mailto:
[email protected]<mailto:[email protected]>>>>>
> > > > > > Sent: Tuesday, March 13, 2018 6:23:24 PM
> > > > > >
> > > > > > To: davidaknowles/leafcutter
> > > > > > Cc: Seyfi, Marilyn; Comment
> > > > > > Subject: Re: [davidaknowles/leafcutter] small sample size
> > affecting
> > > > > > cluster significance detection? (#56)
> > > > > >
> > > > > > Could you provide the correct mapping of samples to
conditions?
> > And
> > > > your
> > > > > > strongest "hit" from rMATS and or MISO.
> > > > > >
> > > > > > Best,
> > > > > > Yang
> > > > > >
> > > > > > On Tue, Mar 13, 2018 at 5:21 PM, mh406910 <
> > ***@***.******@***.******@***.***><mailto:
[email protected]<mailto:[email protected]>><mailto:
***@***.******@***.******@***.***>><mailto:
> ***@***.******@***.******@***.***><mailto:
[email protected]<mailto:[email protected]>>><
> > > ***@***.***>>
> > > > > > wrote:
> > > > > >
> > > > > > > Also when I run your program with the replicates unmerged
as
> > > separate
> > > > > > > replicates I get the same error that there are no
significant
> > > > clusters.
> > > > > > > MISO and rMATS both report otherwise.
> > > > > > >
> > > > > > > Get Outlook for Android<https://aka.ms/ghei36>
> > > > > > >
> > > > > > > ________________________________
> > > > > > > From: goldenflaw ***@***.******@***.***><mailto:
[email protected]<mailto:[email protected]>><mailto:
***@***.******@***.******@***.***>><mailto:
> ***@***.******@***.******@***.***><mailto:
[email protected]<mailto:[email protected]>>><mailto:
> > ***@***.******@***.******@***.***><mailto:
[email protected]<mailto:[email protected]>><mailto:
***@***.******@***.******@***.***>>><mailto:
> > > ***@***.******@***.******@***.***><mailto:
[email protected]<mailto:[email protected]>><mailto:
***@***.******@***.******@***.***>><mailto:
> ***@***.******@***.******@***.***><mailto:
[email protected]<mailto:[email protected]>>>>>
> > > > > > > Sent: Tuesday, March 13, 2018 3:02:47 PM
> > > > > > > To: davidaknowles/leafcutter
> > > > > > > Cc: Seyfi, Marilyn; Comment
> > > > > > > Subject: Re: [davidaknowles/leafcutter] small sample size
> > > affecting
> > > > > > > cluster significance detection? (#56)
> > > > > > >
> > > > > > > Your P14WTmut.txt file looks wrong, you only have 2 samples
in
> > > there.
> > > > > > >
> > > > > > > Best,
> > > > > > > Yang
> > > > > > >
> > > > > > > On Fri, Mar 9, 2018 at 9:07 AM, Yang Li <
***@***.******@***.******@***.***><mailto:gol
[email protected]<mailto:[email protected]>>
> ***@***.***>
> > ***@***.***>
> > > ***@***.***>>
> > > > wrote:
> > > > > > >
> > > > > > > > I will have a look at the whole thing.
> > > > > > > >
> > > > > > > > Best,
> > > > > > > > Yang
> > > > > > > >
> > > > > > > > On Mar 9, 2018 8:54 AM, "seyfim" ***@***.******@***.***>
<mailto:[email protected]>
***@***.***>
> ***@***.***>
> > ***@***.***><
> > > ***@***.***>> wrote:
> > > > > > > >
> > > > > > > >> how do I just share one chromosome with you?
> > > > > > > >>
> > > > > > > >> —
> > > > > > > >> You are receiving this because you were mentioned.
> > > > > > > >> Reply to this email directly, view it on GitHub
> > > > > > > >> <https://github.com/davidaknowles/leafcutter/
> > > > > issues/56#issuecomment-
> > > > > > > 371835036>,
> > > > > > > >> or mute the thread
> > > > > > > >> <https://github.com/notifications/unsubscribe-auth/
> > > > > > > AE1piZqBGBpzf2cNNshOQCmtkfMdzzChks5tcpe2gaJpZM4Si2YZ>
> > > > > > > >> .
> > > > > > > >>
> > > > > > > >
> > > > > > >
> > > > > > > —
> > > > > > > You are receiving this because you commented.
> > > > > > > Reply to this email directly, view it on GitHub<
> > > https://github.com/
> > > > > > > davidaknowles/leafcutter#56#issuecomment-372781944>,
> or
> > > mute
> > > > > the
> > > > > > > thread<https://github.com/notifications/unsubscribe-auth/
> > > > > > > AH0qV7HiNDq4nRYq6MBi9a1xWDnMNfEUks5teBfWgaJpZM4Si2YZ>.
> > > > > > >
> > > > > > > —
> > > > > > > You are receiving this because you were mentioned.
> > > > > > > Reply to this email directly, view it on GitHub
> > > > > > > <https://github.com/davidaknowles/leafcutter/
> > > issues/56#issuecomment-
> > > > > > 372838727>,
> > > > > > > or mute the thread
> > > > > > > <https://github.com/notifications/unsubscribe-
auth/AE1pif2tfb_
> > > > > > R056uBWbmrOrB1zLXuxdoks5teEZOgaJpZM4Si2YZ>
> > > > > > > .
> > > > > > >
> > > > > >
> > > > > > —
> > > > > > You are receiving this because you commented.
> > > > > > Reply to this email directly, view it on GitHub<
> > https://github.com/
> > > > > > davidaknowles/leafcutter#56#issuecomment-372839266>,
or
> > mute
> > > > the
> > > > > > thread<https://github.com/notifications/unsubscribe-auth/
> > > > > > AH0qV4a50BHXeGYRRfHWzlaqB1rvfmN4ks5teEbcgaJpZM4Si2YZ>.
> > > > > >
> > > > > > —
> > > > > > You are receiving this because you were mentioned.
> > > > > > Reply to this email directly, view it on GitHub
> > > > > > <#56 (comment)
> > comment-
> > > > > 372839683>,
> > > > > > or mute the thread
> > > > > > <https://github.com/notifications/unsubscribe-auth/
> > > > > AE1piXefiUjlA0HwvzOEvT5OynDQUxMiks5teEdOgaJpZM4Si2YZ>
> > > > > > .
> > > > > >
> > > > >
> > > > > —
> > > > > You are receiving this because you commented.
> > > > > Reply to this email directly, view it on GitHub<
> https://github.com/
> > > > > davidaknowles/leafcutter#56#issuecomment-372840184>, or
> mute
> > > the
> > > > > thread<https://github.com/notifications/unsubscribe-auth/AH0
> qV7Aqc_
> > > > > xXMWmaRAqFAffdAH88FYvWks5teEfKgaJpZM4Si2YZ>.
> > > > >
> > > > > —
> > > > > You are receiving this because you were mentioned.
> > > > > Reply to this email directly, view it on GitHub
> > > > > <#56 (comment)
> comment-
> > > > 372841413>,
> > > > > or mute the thread
> > > > > <https://github.com/notifications/unsubscribe-auth/
> > > > AE1pifjojIveXOgnlLQb8BSregse9Dcvks5teEkNgaJpZM4Si2YZ>
> > > > > .
> > > > >
> > > >
> > > > —
> > > > You are receiving this because you commented.
> > > > Reply to this email directly, view it on GitHub<
https://github.com/
> > > > davidaknowles/leafcutter#56#issuecomment-372842066>, or
mute
> > the
> > > > thread<https://github.com/notifications/unsubscribe-auth/
> > > > AH0qVyVeY6qZqaqwDsXLAfyjgplfknB6ks5teEmqgaJpZM4Si2YZ>.
> > > >
> > > > —
> > > > You are receiving this because you were mentioned.
> > > > Reply to this email directly, view it on GitHub
> > > > <https://github.com/davidaknowles/leafcutter/
issues/56#issuecomment-
> > > 373083237>,
> > > > or mute the thread
> > > > <https://github.com/notifications/unsubscribe-
auth/AE1picyeYN0qgm8x_
> > > 1MbtBCWV5AT8eLNks5teUNwgaJpZM4Si2YZ>
> > > > .
> > > >
> > >
> > > —
> > > You are receiving this because you authored the thread.
> > > Reply to this email directly, view it on GitHub<https://github.com/
> > > davidaknowles/leafcutter#56#issuecomment-373087793>, or mute
> the
> > > thread<https://github.com/notifications/unsubscribe-
> > > auth/AikLJbxBarvHE4PBpQbaL4R-FYiOc51Nks5teUZhgaJpZM4Si2YZ>.
> > >
> > >
> > > ===================================
> > >
> > >
> > > Please consider the environment before printing this e-mail
> > >
> > > Cleveland Clinic is currently ranked as the No. 2 hospital in the
> > country
> > > by U.S. News & World Report (2017-2018). Visit us online at
> > > http://www.clevelandclinic.org for a complete listing of our
> services,
> > > staff and locations. Confidentiality Note: This message is intended
> for
> > use
> > > only by the individual or entity to which it is addressed and may
> > contain
> > > information that is privileged, confidential, and exempt from
> disclosure
> > > under applicable law. If the reader of this message is not the
> intended
> > > recipient or the employee or agent responsible for delivering the
> > message
> > > to the intended recipient, you are hereby notified that any
> > dissemination,
> > > distribution or copying of this communication is strictly
prohibited.
> If
> > > you have received this communication in error, please contact the
> sender
> > > immediately and destroy the material in its entirety, whether
> electronic
> > or
> > > hard copy. Thank you.
> > >
> > > —
> > > You are receiving this because you were mentioned.
> > > Reply to this email directly, view it on GitHub
> > > <#56 (comment)
> > comment-373088665>,
> > > or mute the thread
> > > <https://github.com/notifications/unsubscribe-auth/AE1pidgjz
> > q9SV9YW1Is63NaIjtwNSMBOks5teUb2gaJpZM4Si2YZ>
> > > .
> > >
> >
> > —
> > You are receiving this because you authored the thread.
> > Reply to this email directly, view it on GitHub<
https://github.com/davi
> > daknowles/leafcutter/issues/56#issuecomment-373426027>, or mute the
> > thread<https://github.com/notifications/unsubscribe-auth/Aik
> > LJUmD86LbwVjw_rwMERYtyO6Bixt0ks5teo6NgaJpZM4Si2YZ>.
> >
> >
> > ===================================
> >
> >
> > Please consider the environment before printing this e-mail
> >
> > Cleveland Clinic is currently ranked as the No. 2 hospital in the
> country
> > by U.S. News & World Report (2017-2018). Visit us online at
> > http://www.clevelandclinic.org for a complete listing of our
services,
> > staff and locations. Confidentiality Note: This message is intended
for
> use
> > only by the individual or entity to which it is addressed and may
> contain
> > information that is privileged, confidential, and exempt from
disclosure
> > under applicable law. If the reader of this message is not the
intended
> > recipient or the employee or agent responsible for delivering the
> message
> > to the intended recipient, you are hereby notified that any
> dissemination,
> > distribution or copying of this communication is strictly prohibited.
If
> > you have received this communication in error, please contact the
sender
> > immediately and destroy the material in its entirety, whether
electronic
> or
> > hard copy. Thank you.
> >
> > —
> > You are receiving this because you were mentioned.
> > Reply to this email directly, view it on GitHub
> > <#56 (comment)
> comment-373445540>,
> > or mute the thread
> > <https://github.com/notifications/unsubscribe-auth/AE1piQRwl
> OQtSEbOoIORNeFr0Un8sXFlks5tepuigaJpZM4Si2YZ>
> > .
> >
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub<https://github.com/davi
> daknowles/leafcutter/issues/56#issuecomment-373448275>, or mute the
> thread<https://github.com/notifications/unsubscribe-auth/Aik
> LJRJjEQjxZtUsXPvFOXwhZhiGL6Imks5tep1ygaJpZM4Si2YZ>.
>
>
> ===================================
>
>
> Please consider the environment before printing this e-mail
>
> Cleveland Clinic is currently ranked as the No. 2 hospital in the
country
> by U.S. News & World Report (2017-2018). Visit us online at
> http://www.clevelandclinic.org for a complete listing of our services,
> staff and locations. Confidentiality Note: This message is intended for
use
> only by the individual or entity to which it is addressed and may
contain
> information that is privileged, confidential, and exempt from
disclosure
> under applicable law. If the reader of this message is not the intended
> recipient or the employee or agent responsible for delivering the
message
> to the intended recipient, you are hereby notified that any
dissemination,
> distribution or copying of this communication is strictly prohibited.
If
> you have received this communication in error, please contact the
sender
> immediately and destroy the material in its entirety, whether
electronic
or
> hard copy. Thank you.
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <#56 (comment)-
373448797>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/
AE1piQx0dpuNbNOdXk8aKGXqe3Y7Ltvnks5tep3SgaJpZM4Si2YZ>
> .
>
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub<https://github.com/
davidaknowles/leafcutter#56#issuecomment-373450060>, or mute the
thread<https://github.com/notifications/unsubscribe-
auth/AikLJSYz4JVvW-I6fgEs_fjQtl5pM_5Wks5tep6ngaJpZM4Si2YZ>.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country
by U.S. News & World Report (2017-2018). Visit us online at
http://www.clevelandclinic.org for a complete listing of our services,
staff and locations. Confidentiality Note: This message is intended for
use
only by the individual or entity to which it is addressed and may contain
information that is privileged, confidential, and exempt from disclosure
under applicable law. If the reader of this message is not the intended
recipient or the employee or agent responsible for delivering the message
to the intended recipient, you are hereby notified that any
dissemination,
distribution or copying of this communication is strictly prohibited. If
you have received this communication in error, please contact the sender
immediately and destroy the material in its entirety, whether electronic
or
hard copy. Thank you.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#56 (comment)-
373451522>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AE1piYvjK7I4AcqI3_
fVzNZxQ9Nm8sRrks5tep-wgaJpZM4Si2YZ>
.
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub<https://github.com/
davidaknowles/leafcutter#56#issuecomment-373454962>, or mute the
thread<https://github.com/notifications/unsubscribe-auth/
AikLJcUcmEfIPtEzddd2abZTNUtzgNQYks5teqIXgaJpZM4Si2YZ>.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country
by U.S. News & World Report (2017-2018). Visit us online at
http://www.clevelandclinic.org for a complete listing of our services,
staff and locations. Confidentiality Note: This message is intended for use
only by the individual or entity to which it is addressed and may contain
information that is privileged, confidential, and exempt from disclosure
under applicable law. If the reader of this message is not the intended
recipient or the employee or agent responsible for delivering the message
to the intended recipient, you are hereby notified that any dissemination,
distribution or copying of this communication is strictly prohibited. If
you have received this communication in error, please contact the sender
immediately and destroy the material in its entirety, whether electronic or
hard copy. Thank you.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#56 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AE1piSVaFzXFuQToZisfk5vtuhahb6dHks5teqLRgaJpZM4Si2YZ>
.
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub<#56 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AikLJcfMFkZSw2VX_IFGJc-511qgLaF6ks5teqQbgaJpZM4Si2YZ>.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
from leafcutter.
goldenflaw
commented on September 19, 2024
I ran LeafCutter on you data with the assignments above and obtained
several significant hits, please try again.
Best,
Yang
On Mar 15, 2018 12:27, "seyfim" <[email protected]> wrote:
But I did run leafcutter with the unmerged replicate bam files and I still
was not generating significance. So this is due to my data being paired-end
reads?
On Mar 15, 2018, at 1:25 PM, goldenflaw <[email protected]<mailto:
[email protected]>> wrote:
You are testing differences in splicing between two conditions, if you do
not have at least 2 samples per condition, you cannot use LeafCutter.
On Mar 15, 2018 12:20, "seyfim" <[email protected]<mailto:
[email protected]>> wrote:
Then what am I testing for? The comparison is the whole point of the
analysis. Could you please explain what you mean?
On Mar 15, 2018, at 1:17 PM, goldenflaw <[email protected]<mailto:
[email protected]><mailto:
[email protected]<mailto:[email protected]>>> wrote:
Please use the above assignment to rerun leafcutter (with all 6 samples).
Best,
Yang
On Mar 15, 2018 12:06, "seyfim" <[email protected]<mailto:
[email protected]><mailto:
[email protected]<mailto:[email protected]>>> wrote:
I know what that means, I have paired end sequencing reads...
On Mar 15, 2018, at 1:02 PM, goldenflaw ***@***.***<mailto:
***@***.******@***.***><mailto:
[email protected]>>> wrote:
"Paired-end" data does not refer to paired samples comparisons, it refers
to paired-end reads. Please have a look at the output files when you do
not
match up your samples for comparisons.
Best,
Yang
On Thu, Mar 15, 2018 at 11:58 AM, seyfim ***@***.***<mailto:
***@***.******@***.***><mailto:
[email protected]>>> wrote:
> No, I specifically used commands for paired-end data in both rMATS and
> MISO.
> So, basically I cannot use your tool?
> On Mar 15, 2018, at 12:57 PM, goldenflaw ***@***.***<
mailto:[email protected]><
mailto:[email protected]><
***@***.***><mailto:
> ***@***.******@***.***><mailto:
>
> LeafCutter (and I believe the other tools that you used) does not
support
> paired samples. When I ran your test without pairing, I get some
> significant hits.
>
> Best,
> Yang
>
> On Thu, Mar 15, 2018 at 11:49 AM, seyfim ***@***.***<
mailto:[email protected]><
mailto:[email protected]><
***@***.***><mailto:
> ***@***.******@***.***><mailto:
>
> > Sorry for not being clear!
> > Yes those are the 2 classes but within each class I do a comparison
like
> > the following:
> > P14M3M4Wt_merged.sorted.filtered.bam (1) vs
> P14M3M4Mut_merged.sorted.filtered.bam
> > (1)
> > Or
> > P40M3M4Wt_merged.sorted.filtered.bam (2) vs
> P40M3M4Wt_merged.sorted.filtered.bam
> > (2)
> >
> > I make sure to differentiate the different classes with their
> > corresponding comparisons in my test.junc files and in my intron_diff
> files
> >
> > On Mar 15, 2018, at 11:53 AM, goldenflaw ***@***.***<
mailto:[email protected]><
mailto:[email protected]><
***@***.***><mail
> ***@***.******@***.***><mailto:
> > ***@***.******@***.***><mailto:
***@***.******@***.***><mailto:
[email protected]>>>> wrote:
> >
> > I'm still confused are the assignments as such:
> >
> > P40M3M4Wt_merged.sorted.filtered.bam 2
> >
> > P14M3M4Mut_merged.sorted.filtered.bam 1
> >
> > P40M3M4Wt_merged.sorted.filtered.bam 2
> >
> > P14M3M4Wt_merged.sorted.filtered.bam 1
> >
> > P40M3M4Het_merged.sorted.filtered.bam 2
> >
> > P14M3M4Het_merged.sorted.filtered.bam 1
> >
> >
> >
> >
> > On Wed, Mar 14, 2018 at 11:36 AM, seyfim ***@***.***<
mailto:[email protected]><
mailto:[email protected]><
***@***.***><mail
> ***@***.******@***.***><mailto:
> > ***@***.******@***.***><mailto:
***@***.******@***.***><mailto:
[email protected]>>>> wrote:
> >
> > > I have two sets (either P14M3M4 or P40M3M4) and the comparisons for
> each
> > > set are sample1: Wt, Wt, Mut then sample 2: Mut, Het, Het
respectively
> > > On Mar 14, 2018, at 12:33 PM, goldenflaw ***@***.***<
mailto:[email protected]><
mailto:[email protected]><
***@***.***>
> ***@***.***><mail
> > ***@***.******@***.***><mailto:
***@***.******@***.***><mailto:
[email protected]>>><mailto:
> > > ***@***.******@***.***><mailto:
***@***.******@***.***><mailto:
[email protected]>><mailto:
> ***@***.******@***.***><mailto:
> > >
> > > Thanks, but I'm not sure I understand? Which 3 samples are
condition
1
> > and
> > > which 3 are condition 2?
> > > Best,
> > > Yang
> > >
> > > On Wed, Mar 14, 2018 at 11:21 AM, mh406910 ***@***.***
<mailto:[email protected]>
<mailto:[email protected]>
***@***.***>
> ***@***.***>
> > ***@***.***><
> > > ***@***.***>> wrote:
> > >
> > > > Hello,
> > > >
> > > > So after reviewing the files I did have the correct samples. The
> > > > comparisons are as follows:
> > > >
> > > >
> > > >
> > > > P14M3M4Wt_merged.sorted.filtered.bam vs P14M3M4Mut_merged.sorted.
> > > > filtered.bam
> > > >
> > > > P14M3M4Wt_merged.sorted.filtered.bam vs P14M3M4Het_merged.sorted.
> > > > filtered.bam
> > > >
> > > > P14M3M4Mut_merged.sorted.filtered.bam . vs
> P14M3M4Het_merged.sorted.
> > > > filtered.bam
> > > >
> > > > P40M3M4Wt_merged.sorted.filtered.bam vs P40M3M4Mut_merged.sorted.
> > > > filtered.bam
> > > >
> > > > P40M3M4Wt_merged.sorted.filtered.bam vs P40M3M4Het_merged.sorted.
> > > > filtered.bam
> > > >
> > > > P40M3M4Mut_merged.sorted.filtered.bam vs
P40M3M4Het_merged.sorted.
> > > > filtered.bam
> > > >
> > > >
> > > > Thanks,
> > > > Marilyn E. Seyfi
> > > > Bioinformatics Technologist
> > > > Cleveland Clinic Genomic Medicine Institute
> > > > work email: ***@***.******@***.***><mailto:
***@***.******@***.******@***.***>><mailto:
> ***@***.******@***.******@***.***><mailto:
[email protected]>><mailto:
> > ***@***.******@***.******@***.***><mailto:
> > > > mobile: (740)-603-2131 <(740)%20603-2131> <(740)%20603-2131>
<(740)%20603-2131>
<(740)%20603-2131>
<(740)%20603-2131>
> <(740)%20603-2131>
> > <(740)%20603-2131>
> > > >
> > > >
> > > >
> > > >
> > > > ________________________________
> > > > From: goldenflaw ***@***.***<mailto:
***@***.******@***.***><mailto:
[email protected]>><mailto:
> ***@***.******@***.***><mailto:
> > ***@***.******@***.***><mailto:
***@***.******@***.***><mailto:
[email protected]>>><mailto:
> ***@***.***
> > > com>>
> > > > Sent: Tuesday, March 13, 2018 6:35 PM
> > > >
> > > > To: davidaknowles/leafcutter
> > > > Cc: Seyfi, Marilyn; Comment
> > > > Subject: Re: [davidaknowles/leafcutter] small sample size
affecting
> > > > cluster significance detection? (#56)
> > > >
> > > > These samples are from the leafcutter output that you gave me (
> > > > test_perind_numers.counts.gz
> > > > <https://github.com/davidaknowles/leafcutter/files/1797264/t
> > est_perind_
> > > > numers.counts.gz>
> > > > )
> > > >
> > > > On Tue, Mar 13, 2018 at 5:32 PM, mh406910 <
***@***.******@***.***><mailto:
> ***@***.***>
> > ***@***.***><
> > > ***@***.***>>
> > > > wrote:
> > > >
> > > > > Well those are not correct.. It should be P14Wt or P40Wt
(sample
> 1)
> > vs
> > > > > P14Mut or P40Mut (sample 2)... I included all comparisons in
the
> > .junc
> > > > step
> > > > > and the following intro cluster step --was that incorrect?
> > > > >
> > > > > Get Outlook for Android<https://aka.ms/ghei36>
> > > > >
> > > > > ________________________________
> > > > > From: goldenflaw ***@***.***<mailto:
***@***.******@***.***><mailto:
[email protected]>><mailto:
> ***@***.******@***.***><mailto:
> > ***@***.******@***.***><mailto:
***@***.******@***.***><mailto:
[email protected]>>><mailto:
> > > ***@***.******@***.***><mailto:
***@***.******@***.***><mailto:
[email protected]>><mailto:
> ***@***.******@***.***><mailto:
> > > > > Sent: Tuesday, March 13, 2018 6:27:23 PM
> > > > >
> > > > > To: davidaknowles/leafcutter
> > > > > Cc: Seyfi, Marilyn; Comment
> > > > > Subject: Re: [davidaknowles/leafcutter] small sample size
> affecting
> > > > > cluster significance detection? (#56)
> > > > >
> > > > > I see that you have 6 samples:
> > > > >
> > > > > P40M3M4Wt_merged.sorted.filtered.bam P14M3M4Mut_merged.sorted.
> > > > filtered.bam
> > > > > P40M3M4Mut_merged.sorted.filtered.bam P14M3M4Wt_merged.sorted.
> > > > filtered.bam
> > > > > P40M3M4Het_merged.sorted.filtered.bam P14M3M4Het_merged.sorted.
> > > > > filtered.bam
> > > > >
> > > > >
> > > > > Could you tell me which ones are "condition 1" and which ones
are
> > > > > "condition 2".
> > > > >
> > > > > On Tue, Mar 13, 2018 at 5:25 PM, mh406910 <
> ***@***.******@***.***><mailto:
***@***.******@***.***><mailto:
> > ***@***.***><
> > > ***@***.***>>
> > > > > wrote:
> > > > >
> > > > > > Just to clarify you mean the ban file? As well as the output
> from
> > > rMATS
> > > > > > and MISO with their highest delta pi value for the selected
> sample
> > > > > > comparison?
> > > > > >
> > > > > > Get Outlook for Android<https://aka.ms/ghei36>
> > > > > >
> > > > > > ________________________________
> > > > > > From: goldenflaw ***@***.***<mailto:
***@***.******@***.***><mailto:
[email protected]>><mailto:
> ***@***.******@***.***><mailto:
> > ***@***.******@***.***><mailto:
***@***.******@***.***><mailto:
[email protected]>>><mailto:
> > > ***@***.******@***.***><mailto:
***@***.******@***.***><mailto:
[email protected]>><mailto:
> ***@***.******@***.***><mailto:
> > > > > > Sent: Tuesday, March 13, 2018 6:23:24 PM
> > > > > >
> > > > > > To: davidaknowles/leafcutter
> > > > > > Cc: Seyfi, Marilyn; Comment
> > > > > > Subject: Re: [davidaknowles/leafcutter] small sample size
> > affecting
> > > > > > cluster significance detection? (#56)
> > > > > >
> > > > > > Could you provide the correct mapping of samples to
conditions?
> > And
> > > > your
> > > > > > strongest "hit" from rMATS and or MISO.
> > > > > >
> > > > > > Best,
> > > > > > Yang
> > > > > >
> > > > > > On Tue, Mar 13, 2018 at 5:21 PM, mh406910 <
> > ***@***.******@***.***><mailto:
***@***.******@***.***><mailto:
[email protected]>><mailto:
> ***@***.******@***.***><mailto:
> > > ***@***.***>>
> > > > > > wrote:
> > > > > >
> > > > > > > Also when I run your program with the replicates unmerged
as
> > > separate
> > > > > > > replicates I get the same error that there are no
significant
> > > > clusters.
> > > > > > > MISO and rMATS both report otherwise.
> > > > > > >
> > > > > > > Get Outlook for Android<https://aka.ms/ghei36>
> > > > > > >
> > > > > > > ________________________________
> > > > > > > From: goldenflaw ***@***.***<mailto:
***@***.******@***.***><mailto:
[email protected]>><mailto:
> ***@***.******@***.***><mailto:
> > ***@***.******@***.***><mailto:
***@***.******@***.***><mailto:
[email protected]>>><mailto:
> > > ***@***.******@***.***><mailto:
***@***.******@***.***><mailto:
[email protected]>><mailto:
> ***@***.******@***.***><mailto:
> > > > > > > Sent: Tuesday, March 13, 2018 3:02:47 PM
> > > > > > > To: davidaknowles/leafcutter
> > > > > > > Cc: Seyfi, Marilyn; Comment
> > > > > > > Subject: Re: [davidaknowles/leafcutter] small sample size
> > > affecting
> > > > > > > cluster significance detection? (#56)
> > > > > > >
> > > > > > > Your P14WTmut.txt file looks wrong, you only have 2 samples
in
> > > there.
> > > > > > >
> > > > > > > Best,
> > > > > > > Yang
> > > > > > >
> > > > > > > On Fri, Mar 9, 2018 at 9:07 AM, Yang Li <
***@***.******@***.***><mailto:gol
> ***@***.***>
> > ***@***.***>
> > > ***@***.***>>
> > > > wrote:
> > > > > > >
> > > > > > > > I will have a look at the whole thing.
> > > > > > > >
> > > > > > > > Best,
> > > > > > > > Yang
> > > > > > > >
> > > > > > > > On Mar 9, 2018 8:54 AM, "seyfim" ***@***.***
<mailto:[email protected]>
<mailto:[email protected]>
***@***.***>
> ***@***.***>
> > ***@***.***><
> > > ***@***.***>> wrote:
> > > > > > > >
> > > > > > > >> how do I just share one chromosome with you?
> > > > > > > >>
> > > > > > > >> —
> > > > > > > >> You are receiving this because you were mentioned.
> > > > > > > >> Reply to this email directly, view it on GitHub
> > > > > > > >> <https://github.com/davidaknowles/leafcutter/
> > > > > issues/56#issuecomment-
> > > > > > > 371835036>,
> > > > > > > >> or mute the thread
> > > > > > > >> <https://github.com/notifications/unsubscribe-auth/
> > > > > > > AE1piZqBGBpzf2cNNshOQCmtkfMdzzChks5tcpe2gaJpZM4Si2YZ>
> > > > > > > >> .
> > > > > > > >>
> > > > > > > >
> > > > > > >
> > > > > > > —
> > > > > > > You are receiving this because you commented.
> > > > > > > Reply to this email directly, view it on GitHub<
> > > https://github.com/
> > > > > > > davidaknowles/leafcutter#56#issuecomment-372781944>,
> or
> > > mute
> > > > > the
> > > > > > > thread<https://github.com/notifications/unsubscribe-auth/
> > > > > > > AH0qV7HiNDq4nRYq6MBi9a1xWDnMNfEUks5teBfWgaJpZM4Si2YZ>.
> > > > > > >
> > > > > > > —
> > > > > > > You are receiving this because you were mentioned.
> > > > > > > Reply to this email directly, view it on GitHub
> > > > > > > <https://github.com/davidaknowles/leafcutter/
> > > issues/56#issuecomment-
> > > > > > 372838727>,
> > > > > > > or mute the thread
> > > > > > > <https://github.com/notifications/unsubscribe-
auth/AE1pif2tfb_
> > > > > > R056uBWbmrOrB1zLXuxdoks5teEZOgaJpZM4Si2YZ>
> > > > > > > .
> > > > > > >
> > > > > >
> > > > > > —
> > > > > > You are receiving this because you commented.
> > > > > > Reply to this email directly, view it on GitHub<
> > https://github.com/
> > > > > > davidaknowles/leafcutter#56#issuecomment-372839266>,
or
> > mute
> > > > the
> > > > > > thread<https://github.com/notifications/unsubscribe-auth/
> > > > > > AH0qV4a50BHXeGYRRfHWzlaqB1rvfmN4ks5teEbcgaJpZM4Si2YZ>.
> > > > > >
> > > > > > —
> > > > > > You are receiving this because you were mentioned.
> > > > > > Reply to this email directly, view it on GitHub
> > > > > > <#56 (comment)
> > comment-
> > > > > 372839683>,
> > > > > > or mute the thread
> > > > > > <https://github.com/notifications/unsubscribe-auth/
> > > > > AE1piXefiUjlA0HwvzOEvT5OynDQUxMiks5teEdOgaJpZM4Si2YZ>
> > > > > > .
> > > > > >
> > > > >
> > > > > —
> > > > > You are receiving this because you commented.
> > > > > Reply to this email directly, view it on GitHub<
> https://github.com/
> > > > > davidaknowles/leafcutter#56#issuecomment-372840184>, or
> mute
> > > the
> > > > > thread<https://github.com/notifications/unsubscribe-auth/AH0
> qV7Aqc_
> > > > > xXMWmaRAqFAffdAH88FYvWks5teEfKgaJpZM4Si2YZ>.
> > > > >
> > > > > —
> > > > > You are receiving this because you were mentioned.
> > > > > Reply to this email directly, view it on GitHub
> > > > > <#56 (comment)
> comment-
> > > > 372841413>,
> > > > > or mute the thread
> > > > > <https://github.com/notifications/unsubscribe-auth/
> > > > AE1pifjojIveXOgnlLQb8BSregse9Dcvks5teEkNgaJpZM4Si2YZ>
> > > > > .
> > > > >
> > > >
> > > > —
> > > > You are receiving this because you commented.
> > > > Reply to this email directly, view it on GitHub<
https://github.com/
> > > > davidaknowles/leafcutter#56#issuecomment-372842066>, or
mute
> > the
> > > > thread<https://github.com/notifications/unsubscribe-auth/
> > > > AH0qVyVeY6qZqaqwDsXLAfyjgplfknB6ks5teEmqgaJpZM4Si2YZ>.
> > > >
> > > > —
> > > > You are receiving this because you were mentioned.
> > > > Reply to this email directly, view it on GitHub
> > > > <https://github.com/davidaknowles/leafcutter/
issues/56#issuecomment-
> > > 373083237>,
> > > > or mute the thread
> > > > <https://github.com/notifications/unsubscribe-
auth/AE1picyeYN0qgm8x_
> > > 1MbtBCWV5AT8eLNks5teUNwgaJpZM4Si2YZ>
> > > > .
> > > >
> > >
> > > —
> > > You are receiving this because you authored the thread.
> > > Reply to this email directly, view it on GitHub<https://github.com/
> > > davidaknowles/leafcutter#56#issuecomment-373087793>, or mute
> the
> > > thread<https://github.com/notifications/unsubscribe-
> > > auth/AikLJbxBarvHE4PBpQbaL4R-FYiOc51Nks5teUZhgaJpZM4Si2YZ>.
> > >
> > >
> > > ===================================
> > >
> > >
> > > Please consider the environment before printing this e-mail
> > >
> > > Cleveland Clinic is currently ranked as the No. 2 hospital in the
> > country
> > > by U.S. News & World Report (2017-2018). Visit us online at
> > > http://www.clevelandclinic.org for a complete listing of our
> services,
> > > staff and locations. Confidentiality Note: This message is intended
> for
> > use
> > > only by the individual or entity to which it is addressed and may
> > contain
> > > information that is privileged, confidential, and exempt from
> disclosure
> > > under applicable law. If the reader of this message is not the
> intended
> > > recipient or the employee or agent responsible for delivering the
> > message
> > > to the intended recipient, you are hereby notified that any
> > dissemination,
> > > distribution or copying of this communication is strictly
prohibited.
> If
> > > you have received this communication in error, please contact the
> sender
> > > immediately and destroy the material in its entirety, whether
> electronic
> > or
> > > hard copy. Thank you.
> > >
> > > —
> > > You are receiving this because you were mentioned.
> > > Reply to this email directly, view it on GitHub
> > > <#56 (comment)
> > comment-373088665>,
> > > or mute the thread
> > > <https://github.com/notifications/unsubscribe-auth/AE1pidgjz
> > q9SV9YW1Is63NaIjtwNSMBOks5teUb2gaJpZM4Si2YZ>
> > > .
> > >
> >
> > —
> > You are receiving this because you authored the thread.
> > Reply to this email directly, view it on GitHub<
https://github.com/davi
> > daknowles/leafcutter/issues/56#issuecomment-373426027>, or mute the
> > thread<https://github.com/notifications/unsubscribe-auth/Aik
> > LJUmD86LbwVjw_rwMERYtyO6Bixt0ks5teo6NgaJpZM4Si2YZ>.
> >
> >
> > ===================================
> >
> >
> > Please consider the environment before printing this e-mail
> >
> > Cleveland Clinic is currently ranked as the No. 2 hospital in the
> country
> > by U.S. News & World Report (2017-2018). Visit us online at
> > http://www.clevelandclinic.org for a complete listing of our
services,
> > staff and locations. Confidentiality Note: This message is intended
for
> use
> > only by the individual or entity to which it is addressed and may
> contain
> > information that is privileged, confidential, and exempt from
disclosure
> > under applicable law. If the reader of this message is not the
intended
> > recipient or the employee or agent responsible for delivering the
> message
> > to the intended recipient, you are hereby notified that any
> dissemination,
> > distribution or copying of this communication is strictly prohibited.
If
> > you have received this communication in error, please contact the
sender
> > immediately and destroy the material in its entirety, whether
electronic
> or
> > hard copy. Thank you.
> >
> > —
> > You are receiving this because you were mentioned.
> > Reply to this email directly, view it on GitHub
> > <#56 (comment)
> comment-373445540>,
> > or mute the thread
> > <https://github.com/notifications/unsubscribe-auth/AE1piQRwl
> OQtSEbOoIORNeFr0Un8sXFlks5tepuigaJpZM4Si2YZ>
> > .
> >
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub<https://github.com/davi
> daknowles/leafcutter/issues/56#issuecomment-373448275>, or mute the
> thread<https://github.com/notifications/unsubscribe-auth/Aik
> LJRJjEQjxZtUsXPvFOXwhZhiGL6Imks5tep1ygaJpZM4Si2YZ>.
>
>
> ===================================
>
>
> Please consider the environment before printing this e-mail
>
> Cleveland Clinic is currently ranked as the No. 2 hospital in the
country
> by U.S. News & World Report (2017-2018). Visit us online at
> http://www.clevelandclinic.org for a complete listing of our services,
> staff and locations. Confidentiality Note: This message is intended for
use
> only by the individual or entity to which it is addressed and may
contain
> information that is privileged, confidential, and exempt from
disclosure
> under applicable law. If the reader of this message is not the intended
> recipient or the employee or agent responsible for delivering the
message
> to the intended recipient, you are hereby notified that any
dissemination,
> distribution or copying of this communication is strictly prohibited.
If
> you have received this communication in error, please contact the
sender
> immediately and destroy the material in its entirety, whether
electronic
or
> hard copy. Thank you.
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <#56 (comment)-
373448797>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/
AE1piQx0dpuNbNOdXk8aKGXqe3Y7Ltvnks5tep3SgaJpZM4Si2YZ>
> .
>
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub<https://github.com/
davidaknowles/leafcutter#56#issuecomment-373450060>, or mute the
thread<https://github.com/notifications/unsubscribe-
auth/AikLJSYz4JVvW-I6fgEs_fjQtl5pM_5Wks5tep6ngaJpZM4Si2YZ>.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country
by U.S. News & World Report (2017-2018). Visit us online at
http://www.clevelandclinic.org for a complete listing of our services,
staff and locations. Confidentiality Note: This message is intended for
use
only by the individual or entity to which it is addressed and may contain
information that is privileged, confidential, and exempt from disclosure
under applicable law. If the reader of this message is not the intended
recipient or the employee or agent responsible for delivering the message
to the intended recipient, you are hereby notified that any
dissemination,
distribution or copying of this communication is strictly prohibited. If
you have received this communication in error, please contact the sender
immediately and destroy the material in its entirety, whether electronic
or
hard copy. Thank you.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#56 (comment)-
373451522>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AE1piYvjK7I4AcqI3_
fVzNZxQ9Nm8sRrks5tep-wgaJpZM4Si2YZ>
.
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub<https://github.com/
davidaknowles/leafcutter#56#issuecomment-373454962>, or mute the
thread<https://github.com/notifications/unsubscribe-auth/
AikLJcUcmEfIPtEzddd2abZTNUtzgNQYks5teqIXgaJpZM4Si2YZ>.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country
by U.S. News & World Report (2017-2018). Visit us online at
http://www.clevelandclinic.org for a complete listing of our services,
staff and locations. Confidentiality Note: This message is intended for use
only by the individual or entity to which it is addressed and may contain
information that is privileged, confidential, and exempt from disclosure
under applicable law. If the reader of this message is not the intended
recipient or the employee or agent responsible for delivering the message
to the intended recipient, you are hereby notified that any dissemination,
distribution or copying of this communication is strictly prohibited. If
you have received this communication in error, please contact the sender
immediately and destroy the material in its entirety, whether electronic or
hard copy. Thank you.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#56 (comment)-
373456055>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/
AE1piSVaFzXFuQToZisfk5vtuhahb6dHks5teqLRgaJpZM4Si2YZ>
.
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub<https://github.com/
davidaknowles/leafcutter#56#issuecomment-373457933>, or mute the
thread<https://github.com/notifications/unsubscribe-
auth/AikLJcfMFkZSw2VX_IFGJc-511qgLaF6ks5teqQbgaJpZM4Si2YZ>.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country
by U.S. News & World Report (2017-2018). Visit us online at
http://www.clevelandclinic.org for a complete listing of our services,
staff and locations. Confidentiality Note: This message is intended for use
only by the individual or entity to which it is addressed and may contain
information that is privileged, confidential, and exempt from disclosure
under applicable law. If the reader of this message is not the intended
recipient or the employee or agent responsible for delivering the message
to the intended recipient, you are hereby notified that any dissemination,
distribution or copying of this communication is strictly prohibited. If
you have received this communication in error, please contact the sender
immediately and destroy the material in its entirety, whether electronic or
hard copy. Thank you.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#56 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AE1pidr5aW1H7x4JNiUaasB1rfk5GMYmks5teqSCgaJpZM4Si2YZ>
.
from leafcutter.
Related Issues (20)
- Does Leafviz work on leafcutterMD result? HOT 3
- error in leafcutter_cluster_regtools.py
- Not reproducible results
- Redundant Splice Event Clustering HOT 1
- Confusion about Proper Input File Extension and Content
- Question about applying PCA on intron usage ratios
- example_data missing
- Bug found in hg38 annotation codes file for LeafViz HOT 1
- how to identify the alternative splicing events for differential cluster, such as ES/MXE/IR/Alt5’/Alt3’
- shinyapp leafcutter HOT 1
- enhancement HOT 2
- Behavior of -p --mincluratio: unexpectedly removing intron clusters HOT 1
- Potentially incorrect use of minclureads and minreads HOT 4
- confusion of normalization method for sQTL input date prepare HOT 1
- Alternative splicing signal on tandem duplicated genes HOT 1
- Creating co-splicing networks with leafcutter output?
- this is broken
- differential splicing with continuous independent variable
- Positive splicing events are not be detected HOT 2
- Start and end sites of junctions
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from leafcutter.