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Old 01-06-2011, 11:36 AM   #1
Location: Berkeley California

Join Date: Nov 2010
Posts: 17
Default Bowtie output from paired end reads

How can I use Bowtie to output aligned paired end fastq files as two separate fastq files ie. aligned_1.fastq and aligned_2.fastq. Right now I can only produce a single output file containing both aligned paired end reads.
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