Question: rsem-calculate-expression prints out the help information when trying to run it
0
gravatar for user230613
2.4 years ago by
user230613270
Europe
user230613270 wrote:

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,

rsem • 1.2k views
ADD COMMENTlink modified 2.3 years ago by Biostar ♦♦ 20 • written 2.4 years ago by user230613270

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

ADD REPLYlink written 2.4 years ago by Rohit1.3k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1021 users visited in the last hour