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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