JuncBASE

JuncBASE (Junction-Based Analysis of Splicing Events) is used to identify and classify alternative splicing events from RNA-Seq data. Alternative splicing events are identified from splice junction reads from RNA-Seq read alignments allowing for analysis of unannoated or aberrant alternative splicing. JuncBASE also uses read counts to quantify the relative expression of each isoform and identifies splice events that are significantly differentially expressed across two or more samples. 

Contact: 
Angela Brooks brooks@broadinstitute.org
Publication Info: 
Title: 
A pan-cancer analysis of transcriptome changes associated with somatic mutations in U2AF1 reveals commonly altered splicing events.
Date: 
January 31, 2014
Notes: 
Brooks AN, Choi PS, de Waal L, Sharifnia T, Imielinksi M, Saksena G, Pedamallu CS, Sivachenko A, Rosenberg M, Chmielecki J, Lawrence MS, DeLuca DS, Getz G, Meyerson M. PLOS ONE 9(1): e87361. doi:10.1371/journal.pone.0087361
Tool Info: