Alignment with bowtie doesn't creates .sam file

[Pery]

Hi,

I'm trying to align a fastq.gz file with bowtie.
My script is:
${bowtie_source} --sam --best ${ref_genome} ${fastq_file}

But it doesn't carets a new .sam file.
How to fix the script in order to get a .sam file in a desired directory?

[neavemj]

I think you need to specify the output file. For example, add "-S new_file.sam" to the script.

Cheers,

Matt.