Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Cuffdiff splicing.diff Greg Bioinformatics 1 11-04-2013 04:04 PM
DEXSeq output not convincing r_sitaram RNA Sequencing 10 05-21-2012 04:15 AM
Cuffdiff NOTEST for splicing.diff Greg Bioinformatics 5 11-14-2011 05:22 AM
Why can't cuffdiff identify splicing difference Jolin Bioinformatics 0 10-14-2011 08:30 AM
DESeq Output Plot and Options silverlining Bioinformatics 3 09-19-2011 11:48 PM

Thread Tools
Old 06-22-2012, 07:49 AM   #1
Junior Member
Location: virginia

Join Date: Jun 2012
Posts: 1
Default DEXSeq splicing plot from CuffDiff output

I am new to RNASeq and just followed Nature protocol paper for Tophat-Cufflink for analysis (
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

Highly appreciate your help.
jasmin9x is offline   Reply With Quote
Old 06-25-2012, 01:08 AM   #2
Senior Member
Location: Heidelberg

Join Date: Aug 2010
Posts: 165

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:

Your idea, I guess, would be to use plotDEXSeq in the cuffdiff hits.
areyes is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 05:32 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO