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Old 06-22-2011, 08:19 AM   #1
Nick
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Location: Philadelphia, PA

Join Date: Jun 2009
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Default Unpaired reads in paired data

I have a paired read dataset in sam format. However some of the reads are unpaired with #0 a the end of their names. The flags indicate these are all optical duplicates. Why would I be missing the mate pair reads? Are the duplicates in the pair removed? Was the pair never sequenced?
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