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Old 08-24-2011, 01:32 PM   #3
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Location: San Diego

Join Date: May 2008
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bwa's sampe adds an XT tag to the sam file that indicates if the read is uniquely mapped, or repetitively mapped. So you could pull all of those reads out with awk, get the cluster coordinates, and then pull out all the reads from the .bam that had those coordinates.
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