GenePattern offers a set of tools to support a wide variety of RNA-seq analyses, including short-read mapping, identification of splice junctions, transcript and isoform detection, quantitation, differential expression, quality control metrics, visualization, and file utilities. http://www.broadinstitute.org/cancer/software/genepattern/modules/RNA-seq
RNA-Seq: a revolutionary tool for transcriptomics http://www.nature.com/nrg/journal/v10/n1/abs/nrg2484.html