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Old 04-28-2011, 11:38 PM   #5
Robby
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Location: Germany

Join Date: Mar 2011
Posts: 68
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Thanks for the fast reply, mrfox.

Maybe I do something wrong. I did the following:
1. cufflinks -G ucsc-reference.gtf sample_n.bam (for all samples)
2. cuffdiff ucsc-reference.gtf sample_1.bam sample_2.bam [....] sample_n.bam
3. compare genes.expr (cufflinks) with genes.fpkm_tracking (cuffdiff)

@mrfox: Which values did you compare with each other? Did you perform the same steps described above?
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