Hi, I have been using bowtie with the -S option to align reads to a reference sequence, and get SAM file as the output.
What I want is to get ONLY the aligned reads in the output. Instead I get all of the reads, both aligned and unaligned, in a huge sam file.
I do not see an option to do this. I see an option to create an additional file of aligned reads, but it is not in sam format.
Does anyone know how to do this?
Thanks,
Shane
What I want is to get ONLY the aligned reads in the output. Instead I get all of the reads, both aligned and unaligned, in a huge sam file.
I do not see an option to do this. I see an option to create an additional file of aligned reads, but it is not in sam format.
Does anyone know how to do this?
Thanks,
Shane
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