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Old 07-05-2012, 12:01 PM   #17
Richard Finney
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Location: bethesda

Join Date: Feb 2009
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Sorry for a late response, vinay.
Those reads with no pair in the bam are "orphan reads". See the 05-10-2012 post for outputting orphan reads. "Good" bams should have all pairs whether mapped or not, though sometimes programs drop unmapped reads to save space.
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