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Old 11-23-2011, 05:17 AM   #1
Location: washington DC

Join Date: Oct 2011
Posts: 21
Default Downstream Cuffdiff analysis

Hi guys,

I am working on the downstream analysis of my rna seq data using Cufflinks, Cuffcompare, and Cuffdiff. I basically want to know three simple questions that I am having a lot of difficulty with. many transcripts represent how many genes? many transcripts match previously known reference transcripts?
3.out of these how many isoforms are there?

Which output file should I be using for my quantification? If I use "genes.fpkm.tracking" from Cuffdiff, I notice there are repeated genes in "gene_short_name" -- this is obviously wrong for quantification.

What files should I use to address my 3 questions and why on earth are genes being repeated in "genes.fpkm.tracking"??

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