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

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.
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https://hal.inria.fr/hal-01728770
Contributor : Mikaël Salson <>
Submitted on : Monday, March 12, 2018 - 9:15:50 AM
Last modification on : Wednesday, October 14, 2020 - 3:40:57 AM

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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, BioMed Central, 2017, 18 (1), pp.1-15. ⟨10.1186/s13059-017-1372-2⟩. ⟨hal-01728770⟩

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