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Old 06-19-2012, 07:54 AM   #2
Richard Finney
Senior Member
Location: bethesda

Join Date: Feb 2009
Posts: 689

I'm no expert, but ... I think ..

The index built for your genome (or chromosome) should be able to handle varying sized read lengths as input to bowtie when doing alignment. The index is not specific to the read lengths that you are trying to align.

The introduction in the bowtie documentation mentions an example 36bp test file. The build is not made from this test file, it's just test data made from the genome (or chromsome). If you need 150bp test data ... well, that's another problem ... likely requiring a little custom scripting.
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