align to different ref assembly

[João 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