SEQanswers - View Single Post - How does inner distances(--mate-inner-dist and --mate-std-dev) work in tophat?

Gangcai · 01-28-2010, 08:02 PM

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?

01-28-2010, 08:02 PM	#1
Gangcai Member Location: Shanghai, China Join Date: Nov 2009 Posts: 30	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-2readslength , eg: 300-250=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?