rsem-calculate-expression prints out the help information when trying to run it

Question

[user230613]

Hi there,

I think I'm missing something because after running rsem-prepare-reference, when I run rsem-calculate-expression, rsem outputs the "help" information. Could anyone explain me what is going on? :S

Here are my commands:

rsem-prepare-reference --gtf /shared/genomes/mmusculus_GRCm38/annotation/Mus_musculus.GRCm38.86.gtf --star -p 12  /shared/genomes/mmusculus_GRCm38/genome/Mus_musculus.GRCm38.dna.toplevel.fa ./rsem_index/mouse_ref

rsem-calculate-expression -p 10 --star --output-genome-bam --gzipped-read-file --paired-end --strandedness none /home/sample1_1.fq.gz,/home/sample2_1.fq.gz /home/sample1_2.fq.gz,/home/sample2_2.fq.gz ./rsem_index/mouse_ref try_mmus_rsem

Thank you in advance,

[Rohit]

You did not mention the version of rsem, but there seems to no option called strandedness. Try using "--strand-specific off" instead.