Can bowtie align mates individually if they don't match?

[history_of_robots]

Hello,

I am trying to use Bowtie for paired end read alignment, using SAM as the output format. If mates align within a specified insert size on the same chromosome, then alignments of two mates are reported with flags 99 and 147, or 163 and 83.

I was wondering if there is way to make bowtie to report alignments of mates even if they don't match (i.e. they don't fall into the insert size, potentially on different chromosomes)? I see that there are flag combinations that could allow such report in SAM, but I wasn't able to find settings that could make Bowtie do that.

thanks.

[kmcarr]

Better handling of discordant read pairs is a feature of Bowtie 2. From the FAQ:

Bowtie 2's paired-end alignment mode is more flexible than Bowtie 1's. For example, for pairs that do not align in a paired fashion, it will attempt to find unpaired alignments for each mate.