Alternative-splicing is a regulated biological phenomenon where one gene can give rise to a variety of transcript isoforms. Most human genes are alternatively spliced. RNA-seq, in contrast to microarrays, has made it possible to analyse not only gene-level differential expression but also isoform-level switches in gene expression using the same raw data. The wet-lab methodology is the same for both analyses, with the exception that calling splicing events requires a higher depth of sequencing coverage. In order to bioinformatically analyse and study splicing using RNA-seq data, a menagerie of tools exist, which have been summarised here.
