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Old 07-13-2010, 08:33 AM   #3
Location: Ithaca, NY

Join Date: Apr 2010
Posts: 39

Also, if you did index it, are you sure you indexed correctly? I had the same issue until I made another index for the genome, then it ran fine. If you want to test if it's the reads, only grab one chromosome, index it, and see if it aligns then.
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