Comments (9)
LinAU
commented on September 26, 2024
BTW, I have checked the top10 BC in raw_cb_frequency.txt. I could find them all in my whitelist file manually.
KR,
Lin
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LinAU
commented on September 26, 2024
Here are the top BC in raw_cb_frequency.txt in folder SCASA_My_Project_20240318203735\1ALIGN\Sample_S1_L001_alignout\alevin
CTGTGCTTCGCCAGCA 1252648
AGTGTCAAGCAGCCTC 1155715
ACTGAGTCAATGGTCT 1036019
ATTGGACAGTTAACGA 1009156
GGCTCGACAGCCTATA 908019
GGGACCTCAATGGAAT 887484
TTCCCAGTCTTCAACT 788127
TGCCCTATCAGCCTAA 757341
CTCAGAATCATCGCTC 696810
GTAGGCCGTCCATGAT 690158
CAGGTGCAGACAAGCC 681130
CAGAATCTCGTCCAGG 675500
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nghiavtr
commented on September 26, 2024
Hi @LinAU ,
Thank you for using Scasa.
From your log file and information you provide, it is hard to know the exact issue.
Could you send us a sample of your data which produced the issue? Then we can investigate the issue in details.
Best,
Nghia
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LinAU
commented on September 26, 2024
Dear Nghia,
Thanks! How could I share the the fq file? Is it OK I share with Onedrive?
KR
Lin
…________________________________
发件人: Trung Nghia Vu ***@***.***>
发送时间: Thursday, March 21, 2024 8:18:52 PM
收件人: eudoraleer/scasa ***@***.***>
抄送: Lin Lin ***@***.***>; Mention ***@***.***>
主题: Re: [eudoraleer/scasa] fail in docker: Total 0 white-listed Barcodes (Issue #11)
Hi @LinAU<https://github.com/LinAU> ,
Thank you for using Scasa.
From your log file and information you provide, it is hard to know the exact issue.
Could you send us a sample of your data which produced the issue? Then we can investigate the issue in details.
Best,
Nghia
―
Reply to this email directly, view it on GitHub<#11 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AJNL46MHC2RZXJKNAMQ2FDDYZMXBZAVCNFSM6AAAAABE4K2NKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMJTGQYDQNBXGE>.
You are receiving this because you were mentioned.Message ID: ***@***.***>
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nghiavtr
commented on September 26, 2024
How big the files are? If they are not too big, Onedrive is ok for me.
Please send the link via my email
Nghia
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LinAU
commented on September 26, 2024
Dear Nghia,
Thanks! I have shared it with you via Onedrive.
KR,
Lin
From: Trung Nghia Vu ***@***.***>
Sent: Friday, 22 March 2024 8:52 AM
To: eudoraleer/scasa ***@***.***>
Cc: Lin Lin ***@***.***>; Mention ***@***.***>
Subject: Re: [eudoraleer/scasa] fail in docker: Total 0 white-listed Barcodes (Issue #11)
How big the files are? If they are not too big, Onedrive is ok for me.
Please send the link via my email: ***@***.******@***.***>
Nghia
—
Reply to this email directly, view it on GitHub<#11 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AJNL46O2FRAR5TUC5H5D46DYZPPIXAVCNFSM6AAAAABE4K2NKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMJUGUZDQMZWHA>.
You are receiving this because you were mentioned.Message ID: ***@***.******@***.***>>
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nghiavtr
commented on September 26, 2024
Tks, I have been able to access the files. I will get back to you as soon as I have some news
N
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nghiavtr
commented on September 26, 2024
Hi @LinAU
I have carefully investigated the issue with your input files. Later on I found that the issue was not from Scasa but raised by Alevin.
The problem is that Alevin does not work for the whitelist from 737K-august-2016.txt, as it describes in their webpage (https://salmon.readthedocs.io/en/latest/alevin.html#whitelist):
Not 10x 737k whitelist
This flag does not use the technologically defined whitelisted cellular barcodes provided by 10x, instead it’s a per experiment level list of subsampled cellular barcodes that need to quantified for consistency with other tools for example an input would be a file generated by cellranger with the name barcodes.tsv (uncompressed).
So, following the instruction, you might run cellranger first with your data to get barcodes.tsv, then use it as the input for the whitelist.
Best,
Nghia
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LinAU
commented on September 26, 2024
Thank you very much! I will test it.
KR,
Lin
From: Trung Nghia Vu ***@***.***>
Sent: Tuesday, 26 March 2024 8:42 PM
To: eudoraleer/scasa ***@***.***>
Cc: Lin Lin ***@***.***>; Mention ***@***.***>
Subject: Re: [eudoraleer/scasa] fail in docker: Total 0 white-listed Barcodes (Issue #11)
Hi @LinAU<https://github.com/LinAU>
I have carefully investigated the issue with your input files. Later on I found that the issue was not from Scasa but raised by Alevin.
The problem is that Alevin does not work for the whitelist from 737K-august-2016.txt, as it describes in their webpage (https://salmon.readthedocs.io/en/latest/alevin.html#whitelist):
Not 10x 737k whitelist
This flag does not use the technologically defined whitelisted cellular barcodes provided by 10x, instead it's a per experiment level list of subsampled cellular barcodes that need to quantified for consistency with other tools for example an input would be a file generated by cellranger with the name barcodes.tsv (uncompressed).
So, following the instruction, you might run cellranger first with your data to get barcodes.tsv, then use it as the input for the whitelist.
Best,
Nghia
-
Reply to this email directly, view it on GitHub<#11 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AJNL46PI2Y3MSR3KIO7IJF3Y2G6ODAVCNFSM6AAAAABE4K2NKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMRRGMZDEMZZGI>.
You are receiving this because you were mentioned.Message ID: ***@***.******@***.***>>
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Related Issues (16)
- mkdir errors HOT 3
- Using your tool for single cell data barcoded with split-seq technology and not droplet based HOT 1
- 。
- scasa cli docs: currently scasa only supports hg38 HOT 1
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- Row names with multiple transcripts HOT 2
- Quantification Fails HOT 3
- QOL change: reset command line color changed by die commands in perl script
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- Alevin Failed HOT 10
- Scasa:v1.0.1 docker shows error HOT 3
- no mapped reads in test on SRA sample HOT 1
- So many Error messages: please help HOT 13
- Smart-seq2 full length RNA-seq data HOT 1
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