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Old 11-23-2011, 05:17 AM   #1
apadr007
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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.

1.how many transcripts represent how many genes?
2.how 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"??

thanks
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