> > 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.

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