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Old 08-06-2010, 01:36 PM   #1
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Location: US

Join Date: Aug 2009
Posts: 8
Default Bowtie Paired-end options

Hi everyone,

I just began to use bowtie to map my solexa paired-end reads to a genome. I found that bowtie has three options to specify the orientation of the paired-end reads, --fr, --rf, and --ff. I tried all of them, and found:

--fr, as the default one, can map most of my data onto the genome. For the left ones, --rf and --ff options can map some, but still leave some reads, which can be separately mapped in non-paired-end mode(should I call it single-end mode), but cannot be recognized as Paired-end reads with any of the three options.

Carefully examining those remaining reads, I found most of them are in an orientation of rev-rev. In another word, both ends of each pair are mapped to the reverse strand. Why does bowtie have no --rr option? How can I process those reads in paired-end mode?

THanks a lot!
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