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
------ 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@yale.edumailto:hongyan.an@yale.edu
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@gmail.com.
Best wishes for your project,
Jen Galaxy team
On 10/1/11 5:57 AM, An, Hongyan wrote:
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
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@yale.edumailto:hongyan.an@yale.edu
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:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
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
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.
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@yale.edu ________________________________________ From: Jeremy Goecks [jeremy.goecks@emory.edu] Sent: Tuesday, October 04, 2011 4:04 PM To: Jennifer Jackson Cc: An, Hongyan; galaxy-user@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
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.
galaxy-user@lists.galaxyproject.org
-
An, Hongyan -
Jennifer Jackson -
Jeremy Goecks