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Old 02-10-2010, 03:28 PM   #1
Location: Malmö

Join Date: Sep 2008
Posts: 37
Default align to different ref assembly


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,
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Old 08-05-2010, 05:28 PM   #2
R diggity
Location: Tennessee

Join Date: Jun 2010
Posts: 12

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.
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