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Old 12-01-2011, 01:24 PM   #5
Location: Seattle

Join Date: Jul 2011
Posts: 98

Originally Posted by swbarnes2 View Post
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.
Thanks very much. That's good to know, since I am aligning with bwa.

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