Do the paired-end forward-reverse and reverse-forward (--fr and --rf) parameters work exactly the same in bowtie2? If not what's the difference between them?
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No they are not the same. The first f(r) refers to the upstream mate and the second refers to the downstream mate.
Considering DNA structure (http://academic.brooklyn.cuny.edu/bi...ructure.html):
5'-------------3'
3'-------------5'
It depends on the sequencing technology. Whether it reads each strand of read from 5' end or 3' end.
For example, if it reads both strands from 5' end, the forward sequence will appear first so it is upstream mate and the reverse complement one is downstream. So we have:
Both from 5' => --fr
Both from 3' => --rf
One from 3' end and the other from 5' (both from one strand) => --ffLast edited by milad621; 10-14-2012, 09:41 AM.
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