Hello,

You will need to provide a GTF or GFF3 file to Cuffdiff - this is what
the tool uses as a reference base to build gene, transcript, and if
provided in the annotation attributes, transcript start site and protein
groupings to perform the differential analysis.

More details can be found here:
http://cufflinks.cbcb.umd.edu/manual.html

Our tutorial and other wiki help is linked from here, see "Tools on the Main Server":
http://wiki.galaxyproject.org/Support#Interpreting_scientific_results

Hopefully this helps,

Jen
Galaxy team

On 5/30/13 3:15 PM, Colaneri, Alejandro Cesar wrote:

Hi

I comparing gen expression data (RNA-seq) in Arabidopsis. Different genotypes, different conditions. Since Arabidopsis is very well annotated I decided to do cuffdiff directly after tophat. However when building my workflow I found that the cuffdiff said a gtf file is necessary. Please see the picture in this email, under INPUT FORMAT. My question is if I can still compare my libraries in the way I designed below.

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