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Old 03-07-2011, 08:34 PM   #1
Location: USA

Join Date: Mar 2010
Posts: 55
Default set up TOPHAT run with paired end reads

I want to run TOPHAT with paired end reads (length 80) so I must set the option "-r". If the selected size is approx. 300, I will set this parameter to 300 - (80 * 2) = 140, correct?
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Old 03-08-2011, 05:45 PM   #2
Location: China

Join Date: Mar 2011
Posts: 18

It's correct.

For more details you can read the manual of tophat .
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