title: Identifying differential alternative splicing events from RNA sequencing data using RNASeq-MATS.
abstract: RNA sequencing (RNA-Seq) has emerged as a powerful and increasingly cost-effective technology for analysis of transcriptomes. RNA-Seq has several significant advantages over gene expression microarrays, including its high sensitivity and accuracy, broad dynamic range, nucleotide-level resolution, ability to detect novel mRNA transcripts, and ability to analyze pre-mRNA alternative splicing. A major application of RNA-Seq is to detect differential alternative splicing, i.e., differences in exon splicing patterns among different biological conditions. We recently developed a statistical method multivariate analysis of transcript splicing (MATS) for detecting differential alternative splicing events from RNA-Seq data. Here, we describe a computational pipeline RNASeq-MATS based on the MATS algorithm. This pipeline automatically detects and analyzes differential alternative splicing events corresponding to all major types of alternative splicing patterns from RNA-Seq data.
authors.affiliation: Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, USA.
authors.forename: Juw Won
authors.initials: JW
authors.lastname: Park
authors.forename: Collin
authors.initials: C
authors.lastname: Tokheim
authors.forename: Shihao
authors.initials: S
authors.lastname: Shen
authors.forename: Yi
authors.initials: Y
authors.lastname: Xing
mesh_terms: D000465:Algorithms; D017398:Alternative Splicing; D000818:Animals; D020869:Gene Expression Profiling / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D012322:RNA Precursors / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D012322:RNA Precursors; D012333:RNA, Messenger