Issue running RSEM

Question

[m.radz]

I am trying to run RSEM on my output from STAR. I have vreated the RSEM ref and have it in my working diretory, however when I run RSEM:

rsem-calculate-expression --paired-end --bam -p 16 "$f" RSEMref/ rsem_out/"$base"

I get this error:

rsem-parse-alignments RSEMref/ rsem_out/MR13_S13.temp/MR13_S13 rsem_out/MR13_S13.stat/MR13_S13 MR13_S13_mappedAligned.toTranscriptome.out.bam 3 -tag XM
Cannot open RSEMref/.grp! It may not exist.

However when I look in RSEMref/ there is a .grp file there, why can it not see it?

Answer 1

[swbarnes2]

I think it wants more than just the directory where the files are kept; it wants the prefix of the files too. So if your file is called something.grp, your command line should be

rsem-calculate-expression --paired-end --bam -p 16 "$f" RSEMref/something rsem_out/"$base"