title: FineSplice, enhanced splice junction detection and quantification: a novel pipeline based on the assessment of diverse RNA-Seq alignment solutions.
abstract: Alternative splicing is the main mechanism governing protein diversity. The recent developments in RNA-Seq technology have enabled the study of the global impact and regulation of this biological process. However, the lack of standardized protocols constitutes a major bottleneck in the analysis of alternative splicing. This is particularly important for the identification of exon-exon junctions, which is a critical step in any analysis workflow. Here we performed a systematic benchmarking of alignment tools to dissect the impact of design and method on the mapping, detection and quantification of splice junctions from multi-exon reads. Accordingly, we devised a novel pipeline based on TopHat2 combined with a splice junction detection algorithm, which we have named FineSplice. FineSplice allows effective elimination of spurious junction hits arising from artefactual alignments, achieving up to 99% precision in both real and simulated data sets and yielding superior F1 scores under most tested conditions. The proposed strategy conjugates an efficient mapping solution with a semi-supervised anomaly detection scheme to filter out false positives and allows reliable estimation of expressed junctions from the alignment output. Ultimately this provides more accurate information to identify meaningful splicing patterns. FineSplice is freely available at https://sourceforge.net/p/finesplice/.
authors.affiliation: Cardiovascular Development and Repair Department, Centro Nacional de Investigaciones Cardiovasculares, Madrid, 28029, Spain, Bioinformatics Unit, Centro Nacional de Investigaciones Cardiovasculares, Madrid, 28029, Spain, National Heart and Lung Institute, Imperial College London, London SW7 2AZ, UK, Cardiovascular Biomedical Research Unit, NIHR Royal Brompton and Harefield NHS Foundation Trust, London SW3 6NP, UK, Department of Cardiology, National Heart Centre Singapore, Singapore 168752, Singapore and Cardiovascular and Metabolic Disorders Program, Duke-NUS Graduate Medical School, Singapore 169857, Singapore.
authors.forename: Alberto
authors.initials: A
authors.lastname: Gatto
authors.forename: Carlos
authors.initials: C
authors.lastname: Torroja-Fungairiño
authors.forename: Francesco
authors.initials: F
authors.lastname: Mazzarotto
authors.forename: Stuart A
authors.initials: SA
authors.lastname: Cook
authors.forename: Paul J R
authors.initials: PJ
authors.lastname: Barton
authors.forename: Fátima
authors.initials: F
authors.lastname: Sánchez-Cabo
authors.forename: Enrique
authors.initials: E
authors.lastname: Lara-Pezzi
mesh_terms: D000465:Algorithms; D017398:Alternative Splicing; D022821:RNA Splice Sites; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D022821:RNA Splice Sites