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deweylab / RSEM

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
http://deweylab.biostat.wisc.edu/rsem/
GNU General Public License v3.0
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RSEM uses the supplied prefix differently for RSEM output files vs STAR intermediate output files #166

Open RamRS opened 3 years ago

RamRS commented 3 years ago

Say I run the rsem-calculate-expression command like so:

     rsem-calculate-expression \
     --paired-end \
     --star \
     --star-path /path/to/STAR \
     --keep-intermediate-files \
     --star-gzipped-read-file \
     {input.fq1} {input.fq2} \
     --output-genome-bam \
     /path/to/hg38 \
     sample_name

The RSEM output file are created with the prefix sample_name., like sample_name.transcript.bam but the intermediate STAR output files (such as the Log.out files) are created as sample_nameLog.out, where the prefix is used without a period. If I were to provide sample_name. as the prefix, I get sample_name..transcript.bam, which also necessitates cleanup.

I know I can change the code in the source perl file to fix this - and make sure rsem and STAR files are generate with the same outfile prefix, but I want to make sure that the change I would make would be correct and that maybe this bug could be addressed in a future release of RSEM.

pliu55 commented 3 years ago

Hi @RamRS, thanks for bringing this up. I have it marked and will have it improved in a future release.