Oqtans looks like an interesting tool for analysing RNA-seq data based on Galaxy framework. Unfortunately the server is down. But it did point to another mapping tool which I am curious to try out PALmapper. What piqued my interest is this in the abstract
"align around 7 million reads per hour on a single AMD CPU core (similar speed as TopHat ). Our study for C. elegans furthermore shows that PALMapperPALMapper is considerably more accurate than TopHat (47% and 81%, respectively)." predicts introns with very high sensitivity (72%) and specificity (82%) when using the annotation as ground truth.