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jianhong / ATACseqQC

ATAC-seq Quality Control
https://jianhong.github.io/ATACseqQC/articles/ATACseqQC.html
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Error in TSSEscore calculation #56

Closed pai-vlc closed 1 year ago

pai-vlc commented 1 year ago

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 commented 1 year ago

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

Jianhong.

pai-vlc commented 1 year ago

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

Or the shifted bam?

jianhong commented 1 year ago

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 GitHubhttps://github.com/jianhong/ATACseqQC/issues/56#issuecomment-1631094025, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABLBEA3H3ZCGPQJCMBSTNQDXPV2KRANCNFSM6AAAAAA2GHBHAY. You are receiving this because you commented.Message ID: @.***>

pai-vlc commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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

jianhong commented 1 year ago

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 GitHubhttps://github.com/jianhong/ATACseqQC/issues/56#issuecomment-1631228966, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABLBEA7FYQAL6Y24GJC5SRTXPWFO3ANCNFSM6AAAAAA2GHBHAY. You are receiving this because you commented.Message ID: @.***>

pai-vlc commented 1 year ago

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 commented 1 year ago

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 GitHubhttps://github.com/jianhong/ATACseqQC/issues/56#issuecomment-1631346722, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABLBEAZGLAJK4CYHF7ZLHJTXPWOCHANCNFSM6AAAAAA2GHBHAY. You are receiving this because you commented.Message ID: @.***>

pai-vlc commented 1 year ago

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

pai-vlc commented 1 year ago

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

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

jianhong commented 1 year ago

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 GitHubhttps://github.com/jianhong/ATACseqQC/issues/56#issuecomment-1631389125, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABLBEA4UZYZWSVWEINDYDBDXPWR4DANCNFSM6AAAAAA2GHBHAY. You are receiving this because you commented.Message ID: @.***>

pai-vlc commented 1 year ago

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

jianhong commented 1 year ago

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 commented 1 year ago

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