Hello everyone,
Is it possible to get fastq file as an output file of bowtie tool ?
Thanks.
Is it possible to get fastq file as an output file of bowtie tool ?
Thanks.
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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). -
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.Last edited by ojham; 07-03-2012, 11:27 AM.Comment
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