DiffSplice: The genome-wide detection of differential splicing events with RNA-seq. RNA sequencing is providing an unprecedented visability into genome-wide expression at the transcription level. DiffSplice is a novel tool for discovering and quantitating alternative splicing variants present in an RNA-seq dataset, without relying on annotated transcriptome or pre-determined splice pattern. For two groups of samples, DiffSplice further utilizes a non-parametric permutation test to identify significant differences in expression at both gene level and transcription level. DiffSplice takes as input the SAM files that supply the alignment of the RNA-seq reads on the reference genome, obtained from an RNA-seq aligner like MapSplice. The results of DiffSplice are summarized as a decomposition of the genome and can be visualized using the UCSC genome browser.

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