How Cuffcompare works?

[ngs_agd]

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!

[honey]

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.