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Old 02-10-2010, 04:28 PM   #1
fadista
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Location: Malmö

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Default align to different ref assembly

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,
Joćo
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Old 08-05-2010, 06:28 PM   #2
R diggity
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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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