Entering edit mode
10.4 years ago
Nick
▴
290
Hi
I am trying to call bowtie with the following parameters:
bowtie -q -n 0 -e 80 -l 18 -a -S -m 5 -best -strata <path-to-index> whole_sample.fastq whole_sample.sam
but bowtie bails out showing
Usage: bowtie [options]* <ebwt> {-1 <m1> -2 <m2> | --12 <r> | <s>} [<hit>]
I think the way I am submitting the parameters follows this pattern. What am I doing wrong?
Thanks - this resolved the problem!