Cuffdiff in Galaxy produces "read_group_tracking" files. However, I wonder if 
these files are enough when using 'replicates=T' in cummeRbund or I also need 
"read_groups.info" and "run.info" files in myDir.

I've tried 'replicates(cuff)' with the 'read_group_tracking' files in my 
directory and I get back an empty set, means that cummerbund is not using 
replicates (or I'm doing something wrong!). At this time I don't see other 
option that run cuffdiff locally. At least you have any suggestion or advice 
about how I can get 'info.files' from Galaxy.

Any particular reason why Cuffdiff output files in Galaxy are not ALL the files 
described in the manual tool?

Thanks for you help.


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