total-hits-norm and compatible-hits-norm default setting different in Cufflinks and Cuffdiff

Question

[trakhtenberg]

In the Cufflinks manual (http://cole-trapnell-lab.github.io/cufflinks/cufflinks/#advanced-abundance-estimation-options) it says regarding Cufflinks options that: –compatible-hits-norm is inactive by default whereas –total-hits-norm is active by default

In the Cuffdiff manual (http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/index.html) it says regarding Cuffdiff options that: –compatible-hits-norm is active by default whereas –total-hits-norm is inactive by default

Could someone please confirm that this is accurate? And if so, what is the logic of using opposite options at different steps (Cufflinks and then Cuffdiff): with regard to this parameter it seems that the same option should be used at both steps by default?

[Kevin Blighe]

Same as Upper-quartile normalization option for Cufflinks and Cuffdiff