When working with RNA-seq data, several tools exist to quantify differences in splicing across conditions and to address the significance of those changes (e.g. DEXSeq, MMDIFF). Quiet often though, these tools result in a long list of genes that is difficult to interpret. By relying on transcript level quantifications, SwitchSeq provides a simple (yet powerful) approach to identify, annotate and visualise the most extreme changes in splicing across two different conditions, namely switch events. In brief, switch events are defined as those cases where, for a given gene, the identity of the most abundant transcript changes across conditions:
Identification, annotation and visualisation of extreme changes in splicing from RNA-seq experiments with SwitchSeq. Mar Gonzàlez-Porta, Alvis Brazma. Available in bioRxiv.
Related slides available in Slideshare
SwitchSeq is licensed under GPLv2.
Mar Gonzàlez-Porta: mar@ebi.ac.uk