Trincado Alonso, Juan Luis, 1987-Entizne, Juan CarlosHysenaj, GeraldSingh, Babita, 1986-Skalic, Miha, 1990-Elliott, David, 1947-Eyras Jiménez, Eduardo2018-05-092018-05-092018Trincado JL, Entizne JC, Hysenaj G, Singh B, Skalic M, Elliott DJ et al. SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions. Genome Biol. 2018 Dec;19(1):40. DOI: 10.1186/s13059-018-1417-11474-7596http://hdl.handle.net/10230/34592Despite the many approaches to study differential splicing from RNA-seq, many challenges remain unsolved, including computing capacity and sequencing depth requirements. Here we present SUPPA2, a new method that addresses these challenges, and enables streamlined analysis across multiple conditions taking into account biological variability. Using experimental and simulated data, we show that SUPPA2 achieves higher accuracy compared to other methods, especially at low sequencing depth and short read length. We use SUPPA2 to identify novel Transformer2-regulated exons, novel microexons induced during differentiation of bipolar neurons, and novel intron retention events during erythroblast differentiation.application/pdfeng© The Author(s). 2018. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.info:eu-repo/semantics/articlehttp://dx.doi.org/10.1186/s13059-018-1417-1Differential splicingAlternative splicingRNA-seqBiological variabilityinfo:eu-repo/semantics/openAccess