Mouse exon-exon junction annotation is compiled from Ensembl release
65 transcripts (required for mapping RNA-Seq reads to junctions)
Annotation for all human genes and their exons compiled from Ensembl Release 57 and UCSC Known Genes (hg19) transcripts (required for both generating the MATS input files and detecting alternative splicing events from the mapping results)
Annotation for all mouse genes and their exons compiled from Ensembl Release 65 transcripts (required for both generating the MATS input files and detecting alternative splicing events from the mapping results)