Thank you Jennifer.
I just start working with these things, so I am wondering which minimal value 
of FPKM I should use in the filter tool. Do you have an advice or an example 
that I could look at?
Thank you


Giuseppe Ianiri, Ph.D.
Division of Cell Biology and Biophysics

________________________________
From: Jennifer Jackson [j...@bx.psu.edu]
Sent: Thursday, November 29, 2012 10:51 AM
To: Ianiri, Giuseppe
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] filter for +/- 2-fold difference in expression levels

Hello Giuseppe,

Fold is included in the Cuffdiff output. Section "Differential expression 
tests", first file, column #9.
http://cufflinks.cbcb.umd.edu/manual.html

A tool like " Filter and Sort -> Filter" could be used to subset specific 
values.

Hopefully this helps,

Jen
Galaxy team

On 11/29/12 5:35 AM, Ianiri, Giuseppe wrote:
Hey guys,
I have my Cuffdiff output and I was trying to figure out how to get the data I 
need.
I am interested in the outputs Transcript and Gene differential expressed. Does 
anyone know how to filter for +/- 2-fold difference in expression levels?
Thank you


Giuseppe Ianiri, Ph.D.
Division of Cell Biology and Biophysics
School of Biological Sciences
5100 Rockhill Road
University of Missouri-Kansas City
Kansas City, MO 64110
Email: iani...@umkc.edu<mailto:iani...@umkc.edu>



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http://galaxyproject.org
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