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Old 04-29-2011, 11:31 AM   #1
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Location: USA

Join Date: Apr 2011
Posts: 5
Smile RNA seq analysis in Galaxy

I am new to this RNA seq world. I am trying to analyse my data in Galaxy. I have a couple of questions. I am not sure whether these were already discussed. I used groomer and then did summary statistics and then trimmed a few bases at 5' and 3' ends. Then I used TopHat for mapping.
My questions are:
1. How do I get the information about the number of reads mapped against the reference genome used?
2. If I have replicates ( 3 for treatment and 3 for control) how do I use cuffdiff? What I want is average FPKM/RPKM values for treatment vs controls and then I need to see the differential expression. Can anybody advise me to do the analysis? Thanks in advance.
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