There is an excellent article on how to do differential gene/transcript expression with Tophat and Cufflinks here: http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html This article will answer the questions you've posed below and provides numerous figures that will help you create a workflow to meet your needs. Best, J. On Jul 20, 2012, at 6:39 PM, i b wrote:

ok, im really confused now about cufflinks and its tools.

All I wanted was to look for differentially expressed genes between two samples: treated (2 replicates) and control (one replicate).

can anyone give me a workflow for a similar analysis with the various options chosen?

I have read a lot of different posts where for cuffdiff they have used cufflinks, cuffcompare, cuffmerge or any gtf file as imput together with the bam file. There must be a difference in using all these different file right???

Also: what is the advantage in using cuffcompare and how we compare them: we give all cufflinks or we separate control from treated? Why do we need cuffmerge?isn't it as well combining the cufflinks? when we use cuffcompare or cuffmerge do we mix all cufflinks no matter is they are control or treated ones?

Please don't send me back to the cufflink page (http://cufflinks.cbcb.umd.edu/index.html)...I need more simpler words!!!!!

Thanks, ib ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

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