ATHLATES and Mosaik

[Louis Letourneau]

I was wondering if in the docs the -om option is missing in the description of how to use Mosaik with ATHLATES.

If -om isn't used than only one output for a read pair is given which is not the same behaviour as novoalign.

this option is described here:
https://groups.google.com/forum/#!topic/mosaik-aligner/AsWn4K6VNwg


also I was wondering if anyone tried bowtie with -a -v 0, to align all perfectly matched reads.
I will try it, but if someone already did, I'm curious of their results.

Thanks you
Louis