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Old 06-21-2012, 07:00 AM   #2
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Location: Purdue University, West Lafayette, Indiana

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Technically the "-165" should be the insert size. Well, the absolute value of -165. So "165 bp" is the answer. However this is especially problematic for RNA as you may be mapping cDNA reads derived from spliced mRNA back to genomic DNA. So if your read pairs happen to flank an exon junction or two, you would need to subtract the intron lengths to get the right (or approximately right) answer.

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