Article
DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition.
Genome biology - 28 Dec 2017
Audoux Jérôme, Philippe Nicolas, Chikhi Rayan, Salson Mikaël, Gallopin Mélina, Gabriel Marc, Le Coz Jérémy, Drouineau Emilie, Commes Thérèse, Gautheret Daniel
Abstract excerpt
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...
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