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Old 02-11-2016, 02:20 PM   #4
Brian Bushnell
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Location: Walnut Creek, CA

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Ignore your aligned bam files, and start over with the original fastq files. Align them together at the same time, telling the aligner to use them as R1 and R2 of pairs. That will generate a single paired sam/bam output file that you should subsequently use.
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