Hi,

I don't know much more about this topic, but for your help:  I listed three links, kindly see it.

https://sites.google.com/a/brown.edu/bioinformatics-in-biomed/tophat-and-cufflinks-by-jason

http://ccb.jhu.edu/software/tophat/index.shtml

http://www.broadinstitute.org/cancer/software/genepattern/modules/RNA-seq