Open zhongzheng1999 opened 4 months ago
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.
@kashyapchhatbar @fgvieira
From STAR's manual:
With
--quantMode TranscriptomeSAM
option STAR will output alignments translated into transcript coordinates in theAligned.toTranscriptome.out.bam
file (in addition to alignments in genomic coordinates inAligned.*.sam/bam
files).
So, I'd say that a new file is created. Can you double-check it?
Yes, a new file is created. I modify in the local wrapper.py, gave Aligned.toTranscriptome.out.Bam one output parameter.
If you modified wrapper.py
, it would be great if you could submit a PR.
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 theAligned.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 thewith tempfile.TemporaryDirectory() as tmpdir:
block, you use thecat
command to output specific temporary files as result files. However, I observed that you only provided options such asReadsPerGene.out.tab
,Chimeric.out.junction
,SJ.out.tab
,etc.
, but there is no code for outputtingAligned.toTranscriptome.out.bam.