Genome Biology (Dec 2017)

DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition

  • Jérôme Audoux,
  • Nicolas Philippe,
  • Rayan Chikhi,
  • Mikaël Salson,
  • Mélina Gallopin,
  • Marc Gabriel,
  • Jérémy Le Coz,
  • Emilie Drouineau,
  • Thérèse Commes,
  • Daniel Gautheret

DOI
https://doi.org/10.1186/s13059-017-1372-2
Journal volume & issue
Vol. 18, no. 1
pp. 1 – 15

Abstract

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Abstract 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.