Error in TSSEscore calculation

Question

Error in TSSEscore calculation

pai-vlc opened this issue a year ago · comments

Thanks for developing this pipeline. I have run it successfully with the test file, but when I try with my ATAC-Seq data I am getting an error.

#Transcription Start Site (TSS) Enrichment Score
tsse <- TSSEscore(gal1, txs)
Error in rbind(...) :
number of columns of matrices must match (see arg 27)

My data are from mouse cells, so I change all the libraries to the mm10 build.

Do you know what could have gone wrong?

Thanks

Pepe

JIANHONG OU · Answer 1 · Tue Jul 11 2023 23:58:29 GMT+0800 (China Standard Time)

Thank you for reporting this. Could you please share me the minimal sample data to repeat your error?

Jianhong.

pai-vlc · Answer 2 · Wed Jul 12 2023 00:02:37 GMT+0800 (China Standard Time)

Do you mean the original bam file? It's 4.2 Gb. Is there a way to downsample it?

Or the shifted bam?

JIANHONG OU · Answer 3 · Wed Jul 12 2023 00:25:13 GMT+0800 (China Standard Time)

The files with sample code for repeating the error. You can try to subset the bam file with samtools for example. ``` samtools view -bh -o tmp.bam ori.bam chr19 samtools view -bh -s 0.1 -o out.bam tmp.bam rm tmp.bam ``` Hope this will help. From: pai-vlc ***@***.***> Date: Tuesday, July 11, 2023 at 12:02 PM To: jianhong/ATACseqQC ***@***.***> Cc: jianhong ou ***@***.***>, Comment ***@***.***> Subject: Re: [jianhong/ATACseqQC] Error in TSSEscore calculation (Issue #56) Do you mean the original bam file? It's 4.2 Gb. Is there a way to downsample it? Or the shifted bam? — Reply to this email directly, view it on GitHub<#56 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABLBEA3H3ZCGPQJCMBSTNQDXPV2KRANCNFSM6AAAAAA2GHBHAY>. You are receiving this because you commented.Message ID: ***@***.***>

pai-vlc · Answer 4 · Wed Jul 12 2023 01:05:29 GMT+0800 (China Standard Time)

I will try. Right now I get this error with that code
samtools view -bh -o tmp.bam ori.bam chr19
Error: unexpected symbol in "samtools view"

I'm running this from Rstudio, if that makes a difference

pai-vlc · Answer 5 · Wed Jul 12 2023 01:33:55 GMT+0800 (China Standard Time)

OK. I did it in the command line, and generated a bam.out file. How can I send it to you? I tried dropping it here, but it tells me it does not support this type of files

pai-vlc · Answer 6 · Wed Jul 12 2023 01:37:39 GMT+0800 (China Standard Time)

the bam.out file is very small (8.5 Mb)

JIANHONG OU · Answer 7 · Wed Jul 12 2023 02:35:06 GMT+0800 (China Standard Time)

Could you please first try to play with the bam file to repeat your error? And show me the code you tried and then try to send the bam file via email may OK in this small size. Thank you! Jianhong From: pai-vlc ***@***.***> Date: Tuesday, July 11, 2023 at 1:37 PM To: jianhong/ATACseqQC ***@***.***> Cc: JIANHONG OU ***@***.***>, Comment ***@***.***> Subject: Re: [jianhong/ATACseqQC] Error in TSSEscore calculation (Issue #56) the bam.out file is very small (8.5 Mb) — Reply to this email directly, view it on GitHub<#56 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABLBEA7FYQAL6Y24GJC5SRTXPWFO3ANCNFSM6AAAAAA2GHBHAY>. You are receiving this because you commented.Message ID: ***@***.***>

pai-vlc · Answer 8 · Wed Jul 12 2023 02:51:04 GMT+0800 (China Standard Time)

Interestingly, in the small subset bam file I made I do not get the error. I get the TSSEscore, no issues.
What could be the difference?

JIANHONG OU · Answer 9 · Wed Jul 12 2023 03:11:11 GMT+0800 (China Standard Time)

Then let figure out a method to share the raw bam file. From: pai-vlc ***@***.***> Date: Tuesday, July 11, 2023 at 2:51 PM To: jianhong/ATACseqQC ***@***.***> Cc: JIANHONG OU ***@***.***>, Comment ***@***.***> Subject: Re: [jianhong/ATACseqQC] Error in TSSEscore calculation (Issue #56) Interestingly, in the small subset bam file I made I do not get the error. I get the TSSEscore, no issues. What could be the difference? — Reply to this email directly, view it on GitHub<#56 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABLBEAZGLAJK4CYHF7ZLHJTXPWOCHANCNFSM6AAAAAA2GHBHAY>. You are receiving this because you commented.Message ID: ***@***.***>

pai-vlc · Answer 10 · Wed Jul 12 2023 03:22:19 GMT+0800 (China Standard Time)

I can put the bam file and my r script in a shared dropbox folder. What's a good email for you?

pai-vlc · Answer 11 · Wed Jul 12 2023 03:23:34 GMT+0800 (China Standard Time)

actually, this is the link to the folder with those files.

https://www.dropbox.com/sh/96w90uvdbzcd05r/AAABWMKE8xVoAR6Y3c0_00_3a?dl=0

JIANHONG OU · Answer 12 · Wed Jul 12 2023 04:39:44 GMT+0800 (China Standard Time)

I downloaded the files. You can remove the share links now. Jianhong. From: pai-vlc ***@***.***> Date: Tuesday, July 11, 2023 at 3:23 PM To: jianhong/ATACseqQC ***@***.***> Cc: JIANHONG OU ***@***.***>, Comment ***@***.***> Subject: Re: [jianhong/ATACseqQC] Error in TSSEscore calculation (Issue #56) actually, this is the link to the folder with those files. https://www.dropbox.com/sh/96w90uvdbzcd05r/AAABWMKE8xVoAR6Y3c0_00_3a?dl=0 — Reply to this email directly, view it on GitHub<#56 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABLBEA4UZYZWSVWEINDYDBDXPWR4DANCNFSM6AAAAAA2GHBHAY>. You are receiving this because you commented.Message ID: ***@***.***>

pai-vlc · Answer 13 · Wed Jul 12 2023 04:41:10 GMT+0800 (China Standard Time)

OK. Than you very much for taking the time to help with this.

JIANHONG OU · Answer 14 · Sat Jul 15 2023 00:11:17 GMT+0800 (China Standard Time)

The issue should be fixed in the development version. Please try to install the devel version by

BiocManager::install("jianhong/ATACseqQC")
# check the version number
packageVersion("ATACseqQC") ## should be 1.25.1

Let me know if there is any issue.

pai-vlc · Answer 15 · Sat Jul 15 2023 05:10:22 GMT+0800 (China Standard Time)

That has fixed the problem. Thanks again for your help!