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!
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