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Old 05-24-2016, 10:47 PM   #7
Michael.Ante
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Location: Vienna

Join Date: Oct 2011
Posts: 123
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Hi Ivygreen,

did you receive the same map mass as with cuffdiff? If not, you can use e.g. R to analyse the genes.fpkm_tracking and isoforms.fpkm_tracking files. For instance, you can make a boxplot of the FPKM values.

Could you please post the tophat command you were using for the alignment?

Cheers,

Michael
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