Trouble Passing Parameters To Bowtie

Question

[Nick]

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?

Answer 1

[Ashutosh Pandey]

I am not sure but maybe "-best" should be written as "--best" and "-strata" as "--strata". Check the same for all the parameters that you have mentioned.

[Nick]

Thanks - this resolved the problem!