Using rsem-calculate-expression and STAR: invalid number of arguments?

Question

[mccatamura]

Hi everyone, I am trying to use RSEM and want to use STAR as my aligner. I'm not sure what argument I am missing/using wrong. But I keep getting this error:

Invalid number of arguments!

The online tutorial is not up to date. In fact, I was able to debug many errors by reading through forums. Anyway, here is the command:

 rsem-calculate-expression -p 2 --star-gzipped-read-file --star \
 --star-path /path/to/star/executable --paired-end \
 /path/to/fastq.gz.1 /path/to/fastq.gz.2 \ 
 STAR_genome_dir sample_name_mouse

Thanks in advance for the help/suggestions!

Answer 1

[Shalu Jhanwar]

Without exact command generating the error, it's hard to pinpoint the bug. However, I'd suggest writing the whole command in one line, without the \ character and run it. \ causes issues sometimes.

[mccatamura]

Hi! The actual command does not have the \ character. I added it in the post for readability :(

Answer 2

[zorbax]

Put --paired-end in a different order:

rsem-calculate-expression --star \
    --star-path /path/to/star/executable \
    --paired-end --star-gzipped-read-file -p 2 \
    /path/to/fastq.gz.1 /path/to/fastq.gz.2 \ 
    STAR_genome_dir sample_name_mouse