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?
There are quite a few articles where researchers have compared various tools for identifying deferentially expressed genes in RNA-Seq, and they reached to conclusion that there is no clear consensus about following a single approach. However, they have suggested few factors that might make one approach appear better than the rests based upon experiment. These include number of replicates and heterogeneity of samples. One such article is: Comparison of software packages for detecting differential expression in RNA-seq studies.