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Old 05-05-2015, 11:00 AM   #4
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707
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Adrian,

You can try running repair.sh to split the file into paired and unpaired reads, and then map twice, once for the paired and once for the unpaired, and then merge the bam files. That will allow maximal use of the available information.
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