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Old 01-28-2010, 08:02 PM   #1
Location: Shanghai, China

Join Date: Nov 2009
Posts: 30
Default How does inner distances(--mate-inner-dist and --mate-std-dev) work in tophat?

I am confused about the inner distance setting. From the manual file, it should be set to (fragementlength-2*readslength , eg: 300-2*50=100). But if the distance counting is based on genome location, then the distance between the pairs should be (fragementlength-2*readslength+inserted_introns_length). Does anybody know how tophat manage the intron insertion?
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