New and improved RNA seq aligners

[David Lyon]

Anyone had experiences with the following new and improved RNA seq aligners

http://www-stat.stanford.edu/~kinfai/SpliceMap/

or

http://research-pub.gene.com/gmap/

In both cases they appear to beat hands down the existing RNA seq aligners like Bowtie/TopHat. Also I read somewhere some of these existing RNA seq aligners have problems with readthrough and encroachment???

[cblum]

I just started working on a comparison of different RNA seq tools:
Tophat, pairagon spaln.
I was getting the impression that gsnap is the tool for RNA seq.
Did you try any of these and how did it work for you?