{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,2]],"date-time":"2026-04-02T04:15:41Z","timestamp":1775103341338,"version":"3.50.1"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,4,1]]},"abstract":"<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: \u00a0christoph.dieterich@age.mpg.de<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv656","type":"journal-article","created":{"date-parts":[[2015,11,11]],"date-time":"2015-11-11T01:08:24Z","timestamp":1447204104000},"page":"1094-1096","source":"Crossref","is-referenced-by-count":340,"title":["Specific identification and quantification of circular RNAs from sequencing data"],"prefix":"10.1093","volume":"32","author":[{"given":"Jun","family":"Cheng","sequence":"first","affiliation":[{"name":"Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Strasse 9B, 50931 Cologne, Germany"}]},{"given":"Franziska","family":"Metge","sequence":"additional","affiliation":[{"name":"Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Strasse 9B, 50931 Cologne, Germany"}]},{"given":"Christoph","family":"Dieterich","sequence":"additional","affiliation":[{"name":"Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Strasse 9B, 50931 Cologne, Germany"}]}],"member":"286","published-online":{"date-parts":[[2015,11,9]]},"reference":[{"key":"2023020112011035000_btv656-B1","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"2023020112011035000_btv656-B2","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1186\/s13059-014-0571-3","article-title":"CIRI: an efficient and unbiased algorithm for de novo circular RNA identification","volume":"16","author":"Gao","year":"2015","journal-title":"Genome Biol."},{"key":"2023020112011035000_btv656-B3","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1038\/nbt.2890","article-title":"Detecting and characterizing circular RNAs","volume":"32","author":"Jeck","year":"2014","journal-title":"Nat. Biotechnol."},{"key":"2023020112011035000_btv656-B4","doi-asserted-by":"crossref","first-page":"1829","DOI":"10.1261\/rna.047126.114","article-title":"Circular RNAs: diversity of form and function","volume":"20","author":"Lasda","year":"2014","journal-title":"RNA"},{"key":"2023020112011035000_btv656-B5","volume-title":"aod: Analysis of Overdispersed Data","author":"Lesnoff","year":"2012"},{"key":"2023020112011035000_btv656-B6","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1111\/j.2517-6161.1948.tb00014.x","article-title":"A probability distribution derived from the binomial distribution by regarding the probability of success as variable between the sets of trials","volume":"10","author":"Skellam","year":"1948","journal-title":"J. R. Stat. Soc. Ser. 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