Bowtie Output

[ojham]

Hello everyone,
Is it possible to get fastq file as an output file of bowtie tool ?

Thanks.

[dpryan]

Normally you would feed bowtie a fastq file as input. Presumably you want a fastq file of the unmapped reads or something like that. Just use the -un flag and supply a file name. If, for some reason, you want the aligned reads (or all of them for that matter) from a SAM file in fastq format, you could just write a trivial shell script to do so (presumably this is also true of the original bowtie output format, which I've never used).

[ojham]

Hi, thank you for the response. I need unmapped reads from bowtie output. Can you please, explain using of -un flag in detail. Thank You.

[dpryan]

Have you looked at the appropriate section of the manual page for bowtie1 or bowtie2 (depending on the version you're using)? BTW, you may want --un-conc instead, depending on your reads.