Dear List

I'm about to design a simple experiment (knockout vs wild-type) and we plan to use RNA-Seq.  We're interested in gene expression, for mRNA and microRNAs in particular, and calculating stats for differential expression.

I'm aware of DEseq, DEGseq and edgeR.  I wanted to ask those who have a lot of experience of this type of analysis if they have any advice for experimental design, in particular, the number of replicates they have used and why (I was planning on going for all biological replicates, no technical).

Thanks
Mick



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