Blog:Benchmarking DGE Tools as a Function of Replicates

Question

[support]

Authors recommend at least 6 replicates/condition in an RNA-seq experiment, and up to 12 in studies where identifying the majority of differentially expressed genes is critical. They recommend experiments with greater than 12 replicates should use DESeq, while those with fewer than 12 replicates should use edgeR.

http://blog.genohub.com/benchmarking-differential-gene-expression-tools/

Answer 1

[Antonio R. Franco]

I wonder why they did not included DESeq2 and BitSeq.

I don't have that reference handy, but I can recall a paper mentioning the superiority of BitSeq

[h.mon]

You probably mean this (behind paywall) paper?

[Antonio R. Franco]

Exactly.. That is the paper