It was always the advice that Cufflinks should be run in RABT mode using a reference gene set to guide the assembly of new transcripts.
I've been exploring StringTie as an alternative to cufflinks, and I have to say. I'm very impressed with its speed: A job that took Cufflinks 6.5hours on 8 cores, took StringTie 10 minutes on 4. This is quicker even than the StringTie Author's benchmarks. I wonder if part of the reason for the speed is that I was using a reference geneset (the ensembl 85 gtf). I also wonder if this is why StringTie seems to be failing to assemble some transcripts that Cufflinks does? (and look real to me).
Does anyone else have any expereince on the effect of including a reference transcriptome in a StringTie assembly? What about a StringTie merge?