FeatureCount output

[Shinichiro03]

I run example data.
In my output directory, I can *.filtered.Aligned.GeneTagged.sorted.bam, but without any featureCounts.bam such as *.aligned.sorted.bam.featureCounts *.ex.featureCounts and *.in.featureCounts.
I saw those files in /.temp directory, and can not see any error in the terminal.

Could you please tell me how to solve this issue?
Really appreciate any of your suggestions and help.
Best,
Shin

[cziegenhain]

Hi Shin,

That is expected, the final GeneTagged bam file contains both the exon and intron gene information derived from featureCounts:

https://github.com/sdparekh/zUMIs/wiki/Output#explanation-of-the-bam-tags-zumis-uses

Best,
Christoph

[Shinichiro03]

Hi Christoph,

Thank you for your reply.
Should I use *.filtered.Aligned.GeneTagged.sorted.bam for running ss3iso?
This is because ss3iso option part mention that "Use '*filtered.tagged.Aligned.out.bam.ex.featureCounts.UBfix.sort.bam' generated by zUMIs. Every read should have a UB:Z tag.”

Best,
Shin

[cziegenhain]

Hi Shin,

yes this is the appropriate bam file.
since it seems this is smartseq3 data, I do strongly recommend to use the UMI error correction in zUMIs.
In case of issues or doubt with other scripts like ss3iso please refer to those GitHub repositories.

Best
Christoph

[Shinichiro03]

Hi Christoph,

Thank you very much for your help!

Best,
Shin

[Shinichiro03]

Hi Christoph, Thank you for your reply. Should I use *.filtered.Aligned.GeneTagged.sorted.bam for running ss3iso? This is because ss3iso option part mention that "Use '*filtered.tagged.Aligned.out.bam.ex.featureCounts.UBfix.sort.bam' generated by zUMIs. Every read should have a UB:Z tag.” Best, Shin

…

On Jun 23, 2022, at 2:46 AM, cziegenhain ***@***.***> wrote: Hi Shin, That is expected, the final GeneTagged bam file contains both the exon and intron gene information derived from featureCounts: https://github.com/sdparekh/zUMIs/wiki/Output#explanation-of-the-bam-tags-zumis-uses <https://github.com/sdparekh/zUMIs/wiki/Output#explanation-of-the-bam-tags-zumis-uses> Best, Christoph — Reply to this email directly, view it on GitHub <#322 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AZYHHVN5AUUTBJQID6DUCL3VQQI4NANCNFSM5ZR7EGXQ>. You are receiving this because you are subscribed to this thread.

[cziegenhain]

Sounds correct, yes!