Hi,

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.