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
I have read a lot of different posts where for cuffdiff they have
used cufflinks, cuffcompare, cuffmerge or any gtf file as imput
together with the bam file.
There must be a difference in using all these different file right???
what is the advantage in using cuffcompare and how we compare them: we
give all cufflinks or we separate control from treated?
Why do we need cuffmerge?isn't it as well combining the cufflinks?
when we use cuffcompare or cuffmerge do we mix all cufflinks no matter
is they are control or treated ones?
Please don't send me back to the cufflink page
(http://cufflinks.cbcb.umd.edu/index.html)...I need more simpler
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