DEXSeq splicing plot from CuffDiff output

jasmin9x

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Join Date: Jun 2012

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DEXSeq splicing plot from CuffDiff output

06-22-2012, 07:49 AM

I am new to RNASeq and just followed Nature protocol paper for Tophat-Cufflink for analysis (http://www.nature.com/nprot/journal/....2012.016.html).
Now I want to get alternative splicing visualization that is not described in that paper. I don't know how to do that or better tool for that. I came across DEXSeq and manual shows similar plots but have no Idea how to do so from my analysis output or data.
Please help me to get those type of graphs as shown on Page 10 on DEXSeq manual at http://watson.nci.nih.gov/bioc_mirro...doc/DEXSeq.pdf

Highly appreciate your help.
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areyes

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06-25-2012, 01:08 AM

If you want to use the plotting function of DEXSeq, the vignette that you posted has the instructions to make them. You have to make an ExonCountSet object with your data, you can find an example of how to do this in the pasilla data package vignette:

Bioconductor - Help

http://www.bioconductor.org/packages/release/data/experiment/vignettes/pasilla/inst/doc/create_objects.pdf

The Bioconductor project aims to develop and share open source software for precise and repeatable analysis of biological data. We foster an inclusive and collaborative community of developers and data scientists.

Your idea, I guess, would be to use plotDEXSeq in the cuffdiff hits.
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DEXSeq splicing plot from CuffDiff output

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