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Old 12-01-2011, 01:22 PM   #4
swbarnes2
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Location: San Diego

Join Date: May 2008
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Yup. The other possibility is if you use bwa for alignments. bwa concatenates all the reference sequences together, so if a read hangs off of one reference onto another, it will be given the right chromosome and position, but the 4 flag will also be put in, as a sign that something is not quite right. I'm not sure if other aligners, like bowtie, will do that.
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