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Old 05-06-2010, 02:44 PM   #3
Location: St. Louis

Join Date: Dec 2009
Posts: 76

I'm wondering about this too. If we rely on external means to trim pair end illumina data, and that results in the pair end mates being trimmed to different lengths in some cases, would that cause bwa to crash?

I know about the -q option built into bwa. But in some cases we will have pair end files that were externally trimmed to accomodate other analysis that was done. Can bwa sampe handle that?
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