DiffSplice: the Genome-Wide Detection of Differential Splicing Events with RNA-seq
Yin Hu, Yan Huang, Ying Du, Christian Orellana, Darshan Singh, Amy Johnson, Anais Monroy, Pei-Fen Kuan, Scott Hammond, Liza Makowski, Scott Randell, Derek Chiang, David Hayes, Corbin Jones, Yufeng Liu, Jan Prins and Jinze Liu
Nucleic Acids Research 2012; doi: 10.1093/nar/gks1026
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.