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Article Dans Une Revue Genome Biology Année : 2017

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

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Résumé

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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Dates et versions

hal-01728770 , version 1 (18-12-2020)

Licence

Paternité - CC BY 4.0

Identifiants

Citer

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⟩
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