Hi Maria, More details are needed to help. Would you like to share a history with me? You might also find the tutorials and other resources for RNA-seq analysis we have helpful. Many are linked from here: https://wiki.galaxyproject.org/Support#Tools_on_the_Main_server:_RNA-seq I've also added the latest sheep build to the set of genomes to be indexed for the RNA-seq mapping tools (bowtie & bowtie2). I'll try to include them in the upcoming snapshot if at all possible. But if not this one (is nearing completion), will be added to the next. Please review the help, then send me a share link if the suggested protocols are not addressing your questions (direct). Jen Galaxy team On 2/6/14 9:09 AM, Maria Hoffman wrote:

Hello,

I am new to cuff diff and just got my data output back and it doesn't look like anything is statistically significant. There are three treatment groups with two biological replicates each group. I am not sure if I made an error somewhere along the line, need to adjust the parameters, or if there really could be no change. The samples are from sheep and I have been using the OvisAries3.0 reference I downloaded from UCSC.

Thanks Maria

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