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?

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
From: Jeremy Goecks []
Sent: Tuesday, October 04, 2011 4:04 PM
To: Jennifer Jackson
Cc: An, Hongyan;
Subject: Re: [galaxy-user] Does Cuffdiff support multiple groups analysis

>> I have 3 groups of accepted hits, each group has 3 replicates. When I add 3 
>> groups with corresponding replicates, the cuffdiff output only gave 2 groups 
>> comparison of differential expression, Please help me here


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


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