ArticleGenome biology2017
DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition.
Article in Genome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Article
- MKMC enables reference-free transcriptomic analysis using k-mer representations.bioRxiv : the preprint server for biology · 2026Article
- Reference-free RNA profiling predicts triple negative breast cancer chemoresistance to neoadjuvant treatment.NAR cancer · 2025Article
- Article
- Acute myeloid leukemia risk stratification in younger and older patients through transcriptomic machine learning models.Scientific reports · 2025Article
- Pseudoassembly of k-mers.bioRxiv : the preprint server for biology · 2025Article
- Distribution rules of 8-mer spectra and characterization of evolution state in animal genome sequences.BMC genomics · 2024Article
- Reference-free inferring of transcriptomic events in cancer cells on single-cell data.BMC cancer · 2024Article
- KaMRaT: a C++ toolkit for k-mer count matrix dimension reduction.Bioinformatics (Oxford, England) · 2024Article
- SPRISS: approximating frequent k-mers by sampling reads, and applications.Bioinformatics (Oxford, England) · 2022Article
- The contribution of uncharted RNA sequences to tumor identity in lung adenocarcinoma.NAR cancer · 2022Article
- kmtricks: efficient and flexible construction of Bloom filters for large sequencing data collections.Bioinformatics advances · 2022Article
- MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data.Genome biology · 2021Article
- Article
- Kmerator Suite: design of specificNAR genomics and bioinformatics · 2021Article
- 2-kupl: mapping-free variant detection from DNA-seq data of matched samples.BMC bioinformatics · 2021Article
- Article
- Comparative genome analysis using sample-specific string detection in accurate long reads.Bioinformatics advances · 2021Article
- iMOKA: k-mer based software to analyze large collections of sequencing data.Genome biology · 2020Article
- Improved Reference Genome Uncovers Novel Sex-Linked Regions in the Guppy (Poecilia reticulata).Genome biology and evolution · 2020Article
Corrections and comments
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Authors and funding
10 authors.
Funding
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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