> I have patched galaxy to have cuffdiff handle replicates and to do normalization, when that gets merged into the main branch your workflow will be the same except you won't have to merge all of the bam files from each condition together to use cuffdiff.

Hi all,

I merged Rory's changes into galaxy-central, so Cuffdiff now supports replicates. I'll see what I can do for Cuffcompare; in the near-term, repeated merging using Cuffcompare will produce a GTF file that is both correct and usable with Cuffdiff.

Thanks,