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-   -   DEXSeq splicing plot from CuffDiff output (http://seqanswers.com/forums/showthread.php?t=21078)

jasmin9x 06-22-2012 07:49 AM

DEXSeq splicing plot from CuffDiff output
 
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.

areyes 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:

http://www.bioconductor.org/packages...te_objects.pdf

Your idea, I guess, would be to use plotDEXSeq in the cuffdiff hits.


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