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Old 02-07-2014, 01:47 AM   #5
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

There's no need to run Flash on them, just use tophat2 and bowtie2 instead of bowtie1.

For the mean inner distance, just try 0 and see if that produces acceptable results (I recall reading that tophat re-estimates the insert length as it runs, though I can't say I've ever checked if that's correct).
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