JuncBASE: A junction-based analysis of splicing events

JuncBASE 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 and annotated exon coordinates. In addition to the identification of alternative splicing events. 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. JuncBASE was developed to characterize annotated and novel alternative splicing events throughout Drosophila development as well as splice events that are altered upon knockdown of splice factors. It has been further developed and used for alternative splicing analysis in cancer RNA-Seq studies.

If you have further questions, email anbrooks@ucsc.edu.

Current version

See GitHub Repository [link]

How to cite JuncBASE

The method was originally described in:

Brooks AN*, Yang L*, Duff MO, Hansen KD, Park JW, Dudoit S, Brenner SE, and Graveley BR. (2011) Conservation of an RNA Regulatory Map between Drosophila and Mammals. Genome Research 21:193-202 *equal contribution [link]

A standalone manuscript describing the software and improvements is currently in revision:

Angela N. Brooks, Kasper D. Hansen, Angadhjot Hundal, Sandrine Dudoit, Matthew Meyerson, Steven E. Brenner. JuncBASE: a junction-based analysis of splicing events from RNA-Seq data

Older versions

Refer to the included file MANUAL.pdf for instructions and a tutorial.

juncBASE_v0.6.tgz [link]

juncBASE_v0.4.tgz [link]