I just generated a couple of RNA-seq dataset hoping to identify the differentially expressed genes caused by a particular treatment, for instance, 4 weeks of High fat diet treatment.
So I have used the standard procedures to analyze the data such as TopHat, cufflinks, and cuffdiff to identify the DE gene lists, however, what I am unsure about is that do we need to normalize each biological replicate with some housekeeping genes? Just like RT-qPCR? If so, how do we do that in Galaxy?
Thank you so much!