Filter For +/- 2-Fold Difference In Expression Levels

Question: Filter For +/- 2-Fold Difference In Expression Levels

6.0 years ago by

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

rna-seq cuffdiff • 1.4k views

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modified 6.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.0 years ago by Ianiri, Giuseppe • 90

6.0 years ago by

Jennifer Hillman Jackson ♦ 25k

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Jennifer Hillman Jackson ♦ 25k wrote:

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 -- Jennifer Jackson http://galaxyproject.org

ADD COMMENT • link written 6.0 years ago by Jennifer Hillman Jackson ♦ 25k

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 ________________________________ 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 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<mailto:ianirig@umkc.edu> ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org

ADD REPLY • link written 6.0 years ago by Ianiri, Giuseppe • 90

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 -- Jennifer Jackson http://galaxyproject.org

ADD REPLY • link written 6.0 years ago by Jennifer Hillman Jackson ♦ 25k

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