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sdparekh / zUMIs

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
GNU General Public License v3.0
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FeatureCount output #322

Closed Shinichiro03 closed 2 years ago

Shinichiro03 commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

Hi Christoph,

Thank you very much for your help!

Best, Shin

Shinichiro03 commented 1 year ago

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

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cziegenhain commented 1 year ago

Sounds correct, yes!