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Old 01-06-2011, 12:36 PM   #1
godzilla07
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Location: Berkeley California

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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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