How to make Bowtie 2 align the following reads as pairs?

Question

[John Smith]

This is somewhat of a continuation to my previous question here. Apparently, the problem with the paired-end artificial reads is that they have the following orientation:

-----> read 1           -----> read 2
--------------------------------- DNA fragment

Is there a Bowtie 2 configuration that will allow for these reads to be aligned as concordant pairs as opposed to discordant ones?

Answer 1

[K.Nijbroek]

From the manual:

The upstream/downstream mate orientations for a valid paired-end alignment against the forward reference strand. E.g., if --fr is specified and there is a candidate paired-end alignment where mate 1 appears upstream of the reverse complement of mate 2 and the fragment length constraints (-I (The minimum fragment length for valid paired-end alignments) and -X (The maximum fragment length for valid paired-end alignments)) are met, that alignment is valid. Also, if mate 2 appears upstream of the reverse complement of mate 1 and all other constraints are met, that too is valid. --rf likewise requires that an upstream mate1 be reverse-complemented and a downstream mate2 be forward-oriented. --ff requires both an upstream mate 1 and a downstream mate 2 to be forward-oriented. Default: --fr (appropriate for Illumina's Paired-end Sequencing Assay).

So.. --ff?

[lh3]

Interestingly, bowtie2 does not have --rr.

[John Smith]

I will try that. My background is not in biology so it was not clear to me what this section of the manual meant (despite understanding upstream/downstream and reverse complement).