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Old 02-23-2012, 01:37 PM   #4
kmcarr
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Location: USA, Midwest

Join Date: May 2008
Posts: 1,177
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I'm wondering if the problem is not with the assembly but with the mapping. Is bwa the best tool to use here, or were the options used appropriate? (I'm asking because I'm not that familiar with bwa.) Frankly, if I had a set of contigs (putative transcripts) and wanted to map raw 454 reads back to them just to count I would use blat.
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