DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition.
Identifieur interne : 000A36 ( PubMed/Corpus ); précédent : 000A35; suivant : 000A37DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition.
Auteurs : Jérôme Audoux ; Nicolas Philippe ; Rayan Chikhi ; Mikaël Salson ; Mélina Gallopin ; Marc Gabriel ; Jérémy Le Coz ; Emilie Drouineau ; Thérèse Commes ; Daniel GautheretSource :
- Genome biology [ 1474-760X ] ; 2017.
English descriptors
- KwdEn :
- Alleles, Computational Biology (methods), Gene Expression Profiling, Gene Expression Regulation, Genetic Variation, High-Throughput Nucleotide Sequencing, Humans, Polyadenylation, RNA (genetics), RNA Splicing, RNA, Antisense, RNA, Long Noncoding (genetics), RNA, Messenger (genetics), Reproducibility of Results, Sequence Analysis, RNA, Software, Transcriptome.
- MESH :
- chemical , genetics : RNA, RNA, Long Noncoding, RNA, Messenger.
- methods : Computational Biology.
- Alleles, Gene Expression Profiling, Gene Expression Regulation, Genetic Variation, High-Throughput Nucleotide Sequencing, Humans, Polyadenylation, RNA Splicing, RNA, Antisense, Reproducibility of Results, Sequence Analysis, RNA, Software, Transcriptome.
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.
DOI: 10.1186/s13059-017-1372-2
PubMed: 29284518
Links to Exploration step
pubmed:29284518Le document en format XML
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<front><div type="abstract" xml:lang="en">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.</div>
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