{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,3]],"date-time":"2026-06-03T14:03:45Z","timestamp":1780495425995,"version":"3.54.1"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2017,10,27]],"date-time":"2017-10-27T00:00:00Z","timestamp":1509062400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002347","name":"BMBF","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Alternative splicing is a biological process of fundamental importance in most eukaryotes. It plays a pivotal role in cell differentiation and gene regulation and has been associated with a number of different diseases. The widespread availability of RNA-Sequencing capacities allows an ever closer investigation of differentially expressed isoforms. However, most tools for differential alternative splicing (DAS) analysis do not take split reads, i.e. the most direct evidence for a splice event, into account. Here, we present DIEGO, a compositional data analysis method able to detect DAS between two sets of RNA-Seq samples based on split reads.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>The python tool DIEGO works without isoform annotations and is fast enough to analyze large experiments while being robust and accurate. We provide python and perl parsers for common formats.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>The software is available at: www.bioinf.uni-leipzig.de\/Software\/DIEGO.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx690","type":"journal-article","created":{"date-parts":[[2017,10,27]],"date-time":"2017-10-27T03:12:53Z","timestamp":1509073973000},"page":"1066-1068","source":"Crossref","is-referenced-by-count":11,"title":["DIEGO: detection of differential alternative splicing using Aitchison\u2019s geometry"],"prefix":"10.1093","volume":"34","author":[{"given":"Gero","family":"Doose","sequence":"first","affiliation":[{"name":"Transcriptome Bioinformatics Group, Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany"},{"name":"Chair of Bioinformatics, Faculty of Mathematics and Computer Science, Leipzig University, Leipzig, Germany"},{"name":"ecSeq Bioinformatics, Leipzig, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephan H","family":"Bernhart","sequence":"additional","affiliation":[{"name":"Transcriptome Bioinformatics Group, Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany"},{"name":"Chair of Bioinformatics, Faculty of Mathematics and Computer Science, Leipzig University, Leipzig, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rabea","family":"Wagener","sequence":"additional","affiliation":[{"name":"Institute of Human Genetics, University of Ulm and University of Ulm Medical Center, Ulm, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steve","family":"Hoffmann","sequence":"additional","affiliation":[{"name":"Transcriptome Bioinformatics Group, Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany"},{"name":"Chair of Bioinformatics, Faculty of Mathematics and Computer Science, Leipzig University, Leipzig, Germany"},{"name":"Computational Biology Group, Leibniz Institute on Ageing - Fritz Lipmann Institute (FLI) and Friedrich-Schiller-University Jena, Jena, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2017,10,27]]},"reference":[{"key":"2023012712471721100_btx690-B1","volume-title":"The Statistical Analysis of Compositional Data, Monographs on Statistics and Applied Probability","author":"Aitchison","year":"1986"},{"key":"2023012712471721100_btx690-B2","doi-asserted-by":"crossref","first-page":"2008","DOI":"10.1101\/gr.133744.111","article-title":"Detecting differential usage of exons from RNA-seq data","volume":"22","author":"Anders","year":"2012","journal-title":"Genome Res"},{"key":"2023012712471721100_btx690-B3","first-page":"e127.","article-title":"Detection and visualization of differential splicing in RNA-seq data with junctionseq","volume":"44","author":"Hartley","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023012712471721100_btx690-B4","doi-asserted-by":"crossref","first-page":"3938","DOI":"10.1093\/bioinformatics\/btv488","article-title":"Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data","volume":"31","author":"Hayer","year":"2015","journal-title":"Bioinformatics"},{"key":"2023012712471721100_btx690-B5","doi-asserted-by":"crossref","first-page":"364","DOI":"10.1186\/s12859-014-0364-4","article-title":"Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems","volume":"15","author":"Liu","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"2023012712471721100_btx690-B6","doi-asserted-by":"crossref","first-page":"862.","DOI":"10.1186\/1471-2164-15-862","article-title":"IUTA: a tool for effectively detecting differential isoform usage from RNA-Seq data","volume":"15","author":"Niu","year":"2014","journal-title":"BMC Genomics"},{"key":"2023012712471721100_btx690-B7","doi-asserted-by":"crossref","first-page":"5311","DOI":"10.1038\/onc.2013.533","article-title":"Hallmarks of alternative splicing in cancer","volume":"33","author":"Oltean","year":"2014","journal-title":"Oncogene"},{"key":"2023012712471721100_btx690-B8","doi-asserted-by":"crossref","first-page":"E5593","DOI":"10.1073\/pnas.1419161111","article-title":"rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data","volume":"111","author":"Shen","year":"2014","journal-title":"PNAS"},{"key":"2023012712471721100_btx690-B9","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1016\/j.bbadis.2008.09.017","article-title":"Alternative splicing and disease","volume":"1792","author":"Tazi","year":"2009","journal-title":"Biochim. 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