This is somewhat of a continuation to my previous question [here][1]. 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?

 [1]: /p/104086/#104104
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 (<a href="http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#bowtie2-options-I">`-I` (The minimum fragment length for valid paired-end alignments)</a> and <a href="http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#bowtie2-options-X">`-X` (The maximum fragment length for valid paired-end alignments)</a>) 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`?