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

Jérôme Audoux (1) , Nicolas Philippe (1) , Rayan Chikhi (2, 3) , Mikael Salson (2, 3) , Mélina Gallopin (4) , Marc Gabriel (5) , Jérémy Le Coz (4) , Emilie Drouineau (4) , Thérèse Commes (1, 6) , Daniel Gautheret (7, 4)

1 Cellules Souches, Plasticité Cellulaire, Médecine Régénératrice et Immunothérapies (IRMB)
2 BONSAI - Bioinformatics and Sequence Analysis
3 CRIStAL - Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189
4 I2BC - Institut de Biologie Intégrative de la Cellule
5 AMMICa - Analyse moléculaire, modélisation et imagerie de la maladie cancéreuse
6 IBC - Institut de Biologie Computationnelle
7 Plateforme de Bioinformatique [Gustave Roussy]

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.

Domaines: Bio-informatique [q-bio.QM]; Algorithme et structure de données [cs.DS]

Jérôme Audoux, Nicolas Philippe, Rayan Chikhi, Mikael Salson, Mélina Gallopin, et al.. DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition. Genome Biology, 2017, 18 (1), pp.1-15. ⟨10.1186/s13059-017-1372-2⟩. ⟨hal-01728770⟩