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Old 05-09-2011, 10:21 PM   #1
ngs_agd
Junior Member
 
Location: India

Join Date: Feb 2011
Posts: 7
Default How Cuffcompare works?

I have used Galaxy to do RNASeq analysis. I don't quite understand the Cuffcompare part.
When running cuffcompare (considering that I am using Cuffdiff afterwards), do I have to provide the 2 assembled transcript files (for the 2 samples on which I want to later run cuffdiff) and a reference file? The reason I am not sure is because when I run cuffdiff, I have to provide the gtf output of cuffcompare and the 2 bam files that I want to run cuffdiff on. I have tried to readup in the galaxy manual without much luck.

Thanks for your help!
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Old 05-10-2011, 12:18 AM   #2
honey
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Location: Pittsburgh

Join Date: Feb 2010
Posts: 151
Default Manual

It look like you have to do lot of readings Just google the term you will find lot of presentations as well as other material. At least you should read
http://cufflinks.cbcb.umd.edu/
If not the Nat Biotechnology paper.
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