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Global and unbiased detection of splice junctions from RNA-seq data
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology, Genomics.ORCID iD: 0000-0001-6085-6749
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology, Genomics.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
2010 (English)In: Genome Biology, ISSN 1474-760X, Vol. 11, no 3, R34- p.Article in journal (Refereed) Published
Abstract [en]

We have developed a new strategy for de novo prediction of splice junctions in short-read RNA-seq data, suitable for detection of novel splicing events and chimeric transcripts. When tested on mouse RNA-seq data, > 31,000 splice events were predicted, of which 88% bridged between two regions separated by <= 100 kb, and 74% connected two exons of the same RefSeq gene. Our method also reports genomic rearrangements such as insertions and deletions.

Place, publisher, year, edition, pages
2010. Vol. 11, no 3, R34- p.
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Medical and Health Sciences
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URN: urn:nbn:se:uu:diva-137747DOI: 10.1186/gb-2010-11-3-r34ISI: 000277309100016OAI: oai:DiVA.org:uu-137747DiVA: diva2:378865
Available from: 2010-12-16 Created: 2010-12-15 Last updated: 2016-02-29Bibliographically approved

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Ameur, AdamFeuk, LarsGyllensten, Ulf

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