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Old 11-29-2011, 07:08 PM   #6
Location: Maryland

Join Date: Apr 2010
Posts: 31

I will try again using the new version (0.7.0a). Before I used 0.6.5a. My only concern is that the manual for the new version on page 39 also says "If a read has one alignment, then the mapping quality is set to 255." Is there another option I should specify to avoid getting a score of 255?
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