ok, im really confused now about cufflinks and its tools.
All I wanted was to look for differentially expressed genes between
two samples: treated (2 replicates) and control (one replicate).
can anyone give me a workflow for a similar analysis with the various
options chosen?
I have read a lot
There is an excellent article on how to do differential gene/transcript
expression with Tophat and Cufflinks here:
http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html
This article will answer the questions you've posed below and provides numerous
figures that will help you
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