Hello, The CuffDiff tool at the main/test public instances and in the last dist should all support multiple groups. If you want detailed help for the Cuff* tools, then the tool author's support list might be able to help: tophat.cufflinks(a)gmail.com. Best wishes for your project, Jen Galaxy team On 10/1/11 5:57 AM, An, Hongyan wrote: -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support

Thanks for your help I did a RNA-seq using galaxy, and find out the transcripts and gene differential expression is identical, furthermore, rest of the file such as CDS, TSS, Promoters etc..are empty files, does not matter if I use annotation file from UCSC refgene gtf file or without annotation file.... What is the possible reason? Regards. Hongyan ------ Hongyan An, Ph.D. Research Associate Genomics Core of Yale Stem Cell Center Yale University School of Medicine 10 Amistad Street Room 203 New Haven, CT 06520 phone: (203)-737-6203 Fax: (203) 785-4305 hongyan.an(a)yale.edu ________________________________________ From: Jeremy Goecks [jeremy.goecks(a)emory.edu] Sent: Tuesday, October 04, 2011 4:04 PM To: Jennifer Jackson Cc: An, Hongyan; galaxy-user(a)bx.psu.edu Subject: Re: [galaxy-user] Does Cuffdiff support multiple groups analysis Hello, Cuffdiff does only pairwise differential expression testing, so each DE test will consider two groups, not three or more. However, Cuffdiff does iterate through and provide data for all possible group pairings. E.g. A vs B A vs C B vs C Best, J.