Comments (8)
Hi, thanks for sharing the details. It seems that you are using Python3.7. Can you please try it again with python 3.5? Some libraries have been changed between Python3.5 and 3.7 which sometimes result in unexpected errors. I would guess that using Python3.5 might be able to fix the problem.
from syri.
Hi, thanks for replying. I got the same errors when using Python3.5.
from syri.
Do you think the whole chromosome inversion can make such an issue?
from syri.
Whole chromosome inversions is not a typical use case. So, it is possible that that there is some uncaught exception. From the output files, it indeed seems that for most chromosomes no syntenic region was identified. If this is indeed the problem, then you can easily solve this by reverse-complimenting the chromosomes for which no syntenic regions were found.
If the problem still persists, then it would be great to see the log file as well as a sample bam file (one chromosome) which can be used to reproduce this error.
from syri.
Thanks. It works now after reverse-complementing the chromosomes with whole chromosome inversion.
I am wondering if I need to adjust the start/end for genome B in syri.out
?
from syri.
Hi. Good to know that it worked for you.
I would recommend that you reverse complement these "inverted" chromosomes in the fasta file itself. Then, you can do alignment and run SyRI again. This will ensure that the coordinates in syri.out
are as per the reverse complemented chromosomes and would reduce chances of errors.
from syri.
Thanks.
Yes, I did the same as you recommended.
Because the genomes I used to analyzed have been published, if I reverse complemented the original fasta files, the syri.out
just record the coordinates of the reverse complemented chromosomes.
I think if I would like to get the coordinates of the original chromosomes, I should adjust the coordinates. Since I only reverse complemented the genome B
, what I need to do is adjust the coordinates of chromosomes in genome B
.
In my case, I would only summarize the rearrangements for the reference genome A
. It would be OK whatever the coordinates of chromosomes in genome B
like.
If people want to draw a local rearrangement between genome A
and genomeB
, I think they should use the coordinates from the original genome so that they can compare with the previous study. Do you think so?
from syri.
It is not possible for me to comment on this.
You are correct in that the coordinates of the genome A would not change, and that you can reverse complement the coordinates from syri.out
to get the original fasta file coordinates. However, it is upto you to decide how you want to report and represent this information :)
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Related Issues (20)
- Removes 'low-quality alignments' - what does this mean? HOT 1
- complicated region not detected correctly HOT 2
- About InvOut and Inv breakpoints HOT 3
- Huge chromosome problem HOT 6
- keyerror HOT 3
- Request for Guidance on Converting NOTALs to Presence in Syri Outputs HOT 3
- translocated to different chromosomes HOT 3
- Consult DUP/INVDP for details HOT 2
- microhomology at ends of insertions HOT 4
- INV vs INVDUP HOT 2
- ERROR syri:201 - Length of query sequence of Chr1 is less than the maximum coordinate of its aligned regions HOT 7
- Wrong CIGAR string HOT 1
- IndexError: list index out of range syri HOT 9
- SYRI:IndexError: list index out of range HOT 1
- how to merge SyRI vcfs HOT 2
- Questions about 'NOTAL' HOT 2
- Question about output
- Support for promer HOT 3
- CIGAR string starting with non-matching base HOT 1
- Overlapping INV and SYN HOT 3
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