I am comparing RNA expression in two groups of rats, a drug treated group 
against a control group. There are 10 biological replicates in each group.  I 
am unsure of how to flow this analysis through Galaxy using Tophat followed by 
Cufflinks/compare/diff. Should the files for each group be merged at any point? 
 I would think they should be kept separate in order to properly account for 
the spread across animals.  I am just a little unsure of how to group the files 
on galaxy, and where to differentiate biological and technical replicates.

On a different note, is there a way to control the bowtie mapping parameters 
more closely when using tophat? 

Thank you for any kind of knowledge on these matters!

-David Martin
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