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Old 01-26-2012, 03:01 PM   #2
chencheni
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Location: china

Join Date: Dec 2011
Posts: 1
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yes. i think bwa is better. if you are working on the mouse genome, while not try to align the sequence to the full genome at first , and then cut the appropriated region you needed. The result will be better than it you mapping to reference sequence directly.
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