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a) map reads against the Drosophila genome (using tophat) (this has already been done to save time)
b) assemble the putative transcripts (using cufflinks) (this has already been done to save time)
c) merge the assemblies (using cuffmerge) (this has already been done to save time)
d) compute differential expression (using cuffdiff) (this has already been done to save time)
e) inspect the results
f) examine the differential expression results (using unix, IGV and cummeRbund)
Extra: g) compare assembled transcripts to annotated transcripts to identify potentially novel ones (using cuffcmp)
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