Why people continue using Tophat if Hisat is available or is Tophat more efficient? ( I read a recent paper using Tophat).
And about cufflinks pipeline, if I do Cufflinks-cuffmerge and Cuffdiff I am doing a double normalization?
Cufflinks use classic-fpkm and Cufdiff a geometric normalization
What do you think of using cufflinks or R package ( Edge R and other) to do DE expression?