Dear all,

I would like to visualise by CummeRbund the Cuffdiff results obtained using the 
cufflinks/cuffdiff workflow on the Galaxy server. My samples include replicates 
data and when I ask for analysis to be done by CummeRbund, to compare 
replicates, I get error messages. From past postings I red that the Galaxy 
Cuffdiff does not allows you to download all the required files  to be used by 
CummeRbund for replicate comparisons. As far as I know, the only way to 
overcome this problem is to run local computer Cuffdiff.  I would like to know 
if anything has changed so far concerning Galaxy Cuffdiff output files and if 
there are other options instead of running local computer Cuffdiff to solve 
this problem.

Any help would be appreciated
Thank you
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