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.
CITATION STYLE
Audoux, J., Philippe, N., Chikhi, R., Salson, M., Gallopin, M., Gabriel, M., … Gautheret, D. (2017). DE-kupl: Exhaustive capture of biological variation in RNA-seq data through k-mer decomposition. Genome Biology, 18(1). https://doi.org/10.1186/s13059-017-1372-2
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