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Old 08-10-2010, 08:11 PM   #4
krobison
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Location: Boston area

Join Date: Nov 2007
Posts: 747
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Thanks for the feedback -- that does give me the idea of trying bwa samse on each original file to see if none, one or both of the paired end files causes trouble.

I'll also re-check that the two files have the same ids in the same order.

THANKS!!
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