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RSEM calculate expression Invalid arguments, but where?

Hi All,

This is my first post on this blog, so I apologise if I don't quite get all the etiquette. I am having a real problem with rsem and whilst the answer appears relatively self-exaplantory from the code, I can't figure out what i'm missing.

rsem-calculate-expression --paired-end \ --star \ --star-path /path/STAR-2.5.3a/bin/MacOSX_x86_64/STAR \ --star-gzipped-read-file \ -p 2 \ /path/VM1018_R1.fastq.gz \ /path/VM1018_R2.fastq.gz \ /genomes/GRCH38_star_ref

I continue to get the error message 'Invalid number of arguments', but I am unsure which non-default I am missing when looking at examples etc.

I am currently running this on RSEM-1.3.0.

I'm sure that the answer is obviously straightforward, but I just can't see it.

Thanks in advance!

Matt

rna-seq rsem
• 4,590 views • link
updated by wuh19850917 • wuh19850917 • written by mad6kj • mad6kj

Please use the code button to format code, commands and such. 101010 Button

rsem-calculate-expression -p 2 --star-gzipped-read-file --paired-end --star \
  --star-path /path/STAR-2.5.3a/bin/MacOSX_x86_64/STAR \ 
  /path/VM1018_R1.fastq.gz /path/VM1018_R2.fastq.gz \
  /genomes/GRCH38_star_ref
• 0 views • link
written by h.mon h.mon

1 answer

Add a sample name at the end of your command

rsem-calculate-expression -p 2 --star-gzipped-read-file --paired-end --star \
  --star-path /path/STAR-2.5.3a/bin/MacOSX_x86_64/STAR \ 
  /path/VM1018_R1.fastq.gz /path/VM1018_R2.fastq.gz \
  /genomes/GRCH38_star_ref VM1018
• 0 views • link
updated by h.mon h.mon • written by wuh19850917 • wuh19850917

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