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Audoux, Jérôme; Philippe, Nicolas; Chikhi, Rayan; Salson, Mikaël; Gallopin, Mélina; Gabriel, Marc; Le Coz, Jérémy; Drouineau, Emilie; Commes, Thérèse; Gautheret, Daniel
Genome Biology, 12/2017, Letnik: 18, Številka: 1Journal Article
We introduce a k-mer-based computational protocol, DE-kupl, for capturing local RNA variation in a set of RNA-seq libraries, independently of a reference genome or transcriptome. DE-kupl extracts all k-mers with differential abundance directly from the raw data files. This enables the retrieval of virtually all variation present in an RNA-seq data set. This variation is subsequently assigned to biological events or entities such as differential long non-coding RNAs, splice and polyadenylation variants, introns, repeats, editing or mutation events, and exogenous RNA. Applying DE-kupl to human RNA-seq data sets identified multiple types of novel events, reproducibly across independent RNA-seq experiments.
