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Old 04-03-2013, 12:05 AM   #3
krispy
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Location: Singapore

Join Date: Apr 2013
Posts: 7
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Thanks for the reply!

But would you mind further explain what do you mean by "lose the benefit of paired end reads"? Does it mean it will be better if I don't cat the two files into one and just let bwa or bowtie to take them separately since bwa/bowtie can recognize them as pair?
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