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Old 10-20-2011, 05:31 AM   #2
Irina Pulyakhina
Location: Oxford

Join Date: Sep 2010
Posts: 24

What kind of aligner do you use? You have paired-end data, so you can have your mate pairs aligned as pairs (and this is the proper way) --> this is number in line 5, or independently --> and is number for "singletons". So for left and right mate pairs you summarize number of alignments within a pair and number of independent alignments -- this is the "... read1" and "... read2".
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