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Old 10-06-2011, 06:28 AM   #3
colindaven
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Location: Germany

Join Date: Oct 2008
Posts: 415
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You have that much sequence of only a few genes ? That seems like a bizarre form of overkill!

I would also align to the whole genome and use mpileup as the previous poster said - there are good instructions on the samtools sourceforge website.
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