Hi,
I want to compare gene deferentially expressed in two conditions (1 and 2). I 
don't have a GTF reference annotation.
In my first attempt, I mapped my Illumina reads with TopHat. Then I run 
Cufflink, and Cuffmerge on my Cufflink outputs for the conditions 1 and 2. At 
the end, I run Cuffdiff using the Cuffmerge output (1 + 2) and the TopHat 
output for the two samples of interest. I got genes and transcripts 
differentially expressed, but I was expecting a quite different output (based 
on the literature).
Do you guys think I did anything wrong?
Also, I am not sure the question makes sense, but is the Cuffmerge step 
essential for the comparison of my two samples? Or could I use my Cufflink 
outputs for samples 1 and 2 for running Cuffdiff?

Regards,


Giuseppe Ianiri
Email: iani...@umkc.edu
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