Hi Guiseppe, This RNA-seq tutorial has an example walk-through using these tools plus links to documentation sources that can help guide you in the analysis, including the paper produced by the tool authors. https://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise And see: http://cufflinks.cbcb.umd.edu/howitworks.html#hdif In short, fold change is the log2 ratio of FPKMs between the two inputs (not simply just a FPKM). If 0, then there is no change; if 1, a 2-fold change, etc. There are also many resources online in general and specific to expression analysis that explain this in more detail. Even if these focus on microarray data, many of the underlying concepts will apply broadly to most (all?) expression analysis, regardless of the technique to obtain the primary data. Good luck, Jen Galaxy team On 11/29/12 10:10 AM, Ianiri, Giuseppe wrote:

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 [jen@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: ianirig@umkc.edu

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