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Old 10-21-2009, 08:27 AM   #2
Cole Trapnell
Senior Member
 
Location: Boston, MA

Join Date: Nov 2008
Posts: 212
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Please note that the RPKM calculation was an experimental feature that is now considered deprecated with the release of Cufflinks. I strongly recommend you discontinue using TopHat to calculate it, and move to Cufflinks instead. The RPKM code will be removed from TopHat in the next release.
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