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Old 08-13-2010, 07:13 AM   #1
Location: united kingdom

Join Date: Feb 2010
Posts: 63
Default TopHat and Cufflinks; closure search

Dear All,
Should cufflinks also include a closure-search option that is included with TopHat?

tophat has;
-r/--mate-inner-dist = distance between paired end reads
--mate-std-dev = std deviation of this distance

and an option to deal with overlapping reads from paired ends

Likewise cufflinks has;
-m = distance between paired end reads
-s = std deviation of this distance

But there is no closure search in cufflinks. As I see overlapping reads in my data and I assume it has happened to other peoples datasets, should cufflinks also have a closure search like tophat?
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