Hello,

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