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.
Genomics Core of Yale Stem Cell Center
Yale University School of Medicine
10 Amistad Street Room 203
New Haven, CT 06520
Fax: (203) 785-4305
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
> 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