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the output files generated by using STAR in snakemake-wrappers should be more comprehensive. #2756

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zhongzheng1999 opened this issue Mar 19, 2024 · 6 comments
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enhancement New feature or request Stale

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@zhongzheng1999
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zhongzheng1999 commented Mar 19, 2024

I'm currently working on setting up a simple RNA-seq analysis pipeline using snakemake, and I've integrated the STAR wrapper from snakemake-wrappers. However, I've run into an issue where specifying --quantMode TranscriptomeSAM prevents me from extracting the Aligned.toTranscriptome.out.bam file as an output. I believe this file is essential for subsequent transcript quantification.

After examining the corresponding wrapper.py file, I noticed that within the with tempfile.TemporaryDirectory() as tmpdir: block, you use the cat command to output specific temporary files as result files. However, I observed that you only provided options such as ReadsPerGene.out.tab, Chimeric.out.junction, SJ.out.tab, etc., but there is no code for outputting Aligned.toTranscriptome.out.bam.

@zhongzheng1999 zhongzheng1999 added the enhancement New feature or request label Mar 19, 2024
@zhongzheng1999
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zhongzheng1999 commented Mar 19, 2024

When I use the --outStd BAM_SortedByCoordinate parameter, the output for {snakemake.output.aln} is the Aligned.out.bam file. However, I'm wondering if using --quantMode TranscriptomeSAM would mean that Aligned.toTranscriptome.out.bam is output instead of Aligned.out.bam. I've checked the STAR documentation but couldn't find an explanation for this issue.

@zhongzheng1999
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@kashyapchhatbar @fgvieira

@fgvieira
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From STAR's manual:

With --quantMode TranscriptomeSAM option STAR will output alignments translated into transcript coordinates in the Aligned.toTranscriptome.out.bam file (in addition to alignments in genomic coordinates in Aligned.*.sam/bam files).

So, I'd say that a new file is created. Can you double-check it?

@zhongzheng1999
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Yes, a new file is created. I modify in the local wrapper.py, gave Aligned.toTranscriptome.out.Bam one output parameter.

@fgvieira
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If you modified wrapper.py, it would be great if you could submit a PR.

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github-actions bot commented Oct 1, 2024

This issue was marked as stale because it has been open for 6 months with no activity.

@github-actions github-actions bot added the Stale label Oct 1, 2024
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