align to different ref assembly

[fadista]

Hi,

I would like to know if someone have tried to map WGS Illumina reads from one species to a reference assembly from other species (like with 20million years divergence). And if so, what were your results and bullet point conclusions? Were there a lot of reads that did not map?

And which settings of your alignment algorithm shall I choose? I believe that I have to accept more than 2 mismatches, since it is an alignment between two species...


Thanks in advance,
João

[R diggity]

It looks like this thread fell under the radar, but I too am facing a similar project. Is there anything like this in the literature? I've looked, but haven't had much luck.