Hi All

I've started analyzing my RNA-Seq data for two time points: Day0 and Day4 for 
control and treated. I've done aligning the data to the reference genome using 
Tophat. I've removed duplicates from the data sets. Could somebody please tell 
me, how important is it to remove duplicates and how will it influence my 
results if I don't remove?

I want to start with Cufflinks all the way through to Cuffdiff. Where do I 
start since there are just so many options (in the manual) to choose from? What 
do I look for?

Kind regards



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