Dear all,

I have Illumina RNAseq data and want to look for differences in gene expression 
between male and female rats and transgenic vs. wildtype; for each condition I 
have triplicates. I mapped with TopHat for Illumina, using the reference genome 
rn5 and default settings. I did Cuffdiff afterwards and used the GTF-file 
Rattus norvegicus.Rnor_5.0.72.gtf as transcript. As result I got no significant 
changes in expression and it always says "NO TEST" (or sometimes "LOW DATA"). I 
found that lowering or raising the -c option might control the cuffdiff 
behavior, but I do not know what it is and how to control it. Can you explain 
me how to do it? And would you advise me to use another transcript for 
Cuffdiff? And when yes, where can I get it?

Lots of questions. Thanks in advance for your answer.

The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at  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:

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

To search Galaxy mailing lists use the unified search at:

Reply via email to