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Medientyp:
E-Artikel
Titel:
Specific identification and quantification of circular RNAs from sequencing data
Beteiligte:
Cheng, Jun;
Metge, Franziska;
Dieterich, Christoph
Erschienen:
Oxford University Press (OUP), 2016
Erschienen in:Bioinformatics
Sprache:
Englisch
DOI:
10.1093/bioinformatics/btv656
ISSN:
1367-4811;
1367-4803
Entstehung:
Anmerkungen:
Beschreibung:
<jats:title>Abstract</jats:title>
<jats:p>Motivation: Circular RNAs (circRNAs) are a poorly characterized class of molecules that have been identified decades ago. Emerging high-throughput sequencing methods as well as first reports on confirmed functions have sparked new interest in this RNA species. However, the computational detection and quantification tools are still limited.</jats:p>
<jats:p>Results: We developed the software tandem, DCC and CircTest. DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies a series of filters and integrates data across replicate sets to arrive at a precise list of circRNA candidates. We assessed the detection performance of DCC on a newly generated mouse brain data set and publicly available sequencing data. Our software achieves a much higher precision than state-of-the-art competitors at similar sensitivity levels. Moreover, DCC estimates circRNA versus host gene expression from counting junction and non-junction reads. These read counts are finally used to test for host gene-independence of circRNA expression across different experimental conditions by our R package CircTest. We demonstrate the benefits of this approach on previously reported age-dependent circRNAs in the fruit fly.</jats:p>
<jats:p>Availability and implementation: The source code of DCC and CircTest is licensed under the GNU General Public Licence (GPL) version 3 and available from https://github.com/dieterich-lab/[DCC or CircTest].</jats:p>
<jats:p>Contact: christoph.dieterich@age.mpg.de</jats:p>
<jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.</jats:p>