With the advent of next-generation sequencing techniques like RNA-Seq, there is the potential for unbiased transcriptome-wide analysis of gene expression and alternative splicing irrespective of the abundance class of the transcript. A potential use for this technology is to help us understand the role that alternative splicing plays in brain region-specific differences. In this study, we focused on two RNA-Seq datasets derived from the mouse brain, one from the striatum and the other from the whole brain.