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Old 04-02-2010, 03:22 PM   #4
lh3
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Location: Boston

Join Date: Feb 2008
Posts: 693
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I usually recommend the default. For 100bp reads, the default allows 5 mismatches/gaps. You may use -n 6 or 7, but not more. If I were analyzing the data, I would throw those ~1-2% reads in the first place. In addition, are these purity filtered reads? Do the reads have poor-quality tail? You may try -q15 to trim the tail. In general, i guess your data is non-typical. For single-end 100bp reads, bwa should map more than 90% to human; with paired-end, even more.
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