OmiRas, a web server (from GenXPro Frankfurt) for the annotation, comparison and visualization of interaction networks of non-coding RNAs derived from small RNA-Sequencing experiments of two different conditions.
http://tools.genxpro.net/omiras
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,...
There are different ways to perform exome sequence analysis, but GATK have a good guide for 'Best Practice': http://www.broadinstitute.org/gatk/guide/best-practices