INSERM U1183 IRMB, Université de Montpellier, Hopital St Eloi, 80 avenue Augustin Fliche, Montpellier, 34295, France.
Institut de Biologie Computationnelle, Université Montpellier, Montpellier, France.
Genome Biol. 2017 Dec 28;18(1):243. doi: 10.1186/s13059-017-1372-2.
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.
我们介绍了一种基于 k-mer 的计算方案 DE-kupl，用于在一组 RNA-seq 文库中捕获局部 RNA 变异，而无需参考基因组或转录组。DE-kupl 从原始数据文件中直接提取具有差异丰度的所有 k-mer。这使得几乎可以检索到 RNA-seq 数据集中存在的所有变异。随后，这些变异被分配到生物事件或实体中，例如差异长非编码 RNA、剪接和多聚腺苷酸化变体、内含子、重复、编辑或突变事件以及外源性 RNA。将 DE-kupl 应用于人类 RNA-seq 数据集，在多个独立的 RNA-seq 实验中可重复鉴定多种类型的新型事件。
