Detection and visualization of differential splicing in RNA-Seq data with JunctionSeq.

ABSTRACT: Although RNA-Seq data provide unprecedented isoform-level expression information, detection of alternative isoform regulation (AIR) remains difficult, particularly when working with an incomplete transcript annotation. We introduce JunctionSeq, a new method that builds on the statistical techniques used by the well-established DEXSeq package to detect differential usage of both exonic regions and splice junctions. In particular, JunctionSeq is capable of detecting differential usage of novel splice junctions without the need for an additional isoform assembly step, greatly improving performance when the available transcript annotation is flawed or incomplete. JunctionSeq also provides a powerful and streamlined visualization toolset that allows bioinformaticians to quickly and intuitively

SUBMITTER: Hartley SW 

PROVIDER: S-EPMC5009739 | biostudies-literature | 2016 Sep

REPOSITORIES: biostudies-literature