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Old 11-25-2013, 01:36 PM   #2
kmcarr
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Location: USA, Midwest

Join Date: May 2008
Posts: 1,155
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Here's your problem.
Quote:
(method=union and stranded=yes)
For libraries prepared using TruSeq Stranded RNA Kits (dUTP second strand marking) you should set htseq-count -stranded=reverse
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