I just came across this blog. Looks very promising. Was just wondering has anyone tried HISAT and StringTie yet? How does HISAT perform compared to other aligning methods (Bowtie2, STAR, GSNAP particularly). And how does StringTie compare to Cufflinks? Did not find any published papers on these, probably they will be out soon. HISAT was released in July 2014 and StringTie in April 2014. It is surprising no one has used (or even heard?) about these tools. There is no mention of these tools anywhere on any forums.
I am going to try and test these myself, just wanted to know if anyone else is at it too.
StringTie paper is out. I am going to use it on a simulated dataset and compare results with that of cuffdiff. Meanwhile I would like to hear if you have any updates on this.