{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,3,7]],"date-time":"2023-03-07T16:52:05Z","timestamp":1678207925368},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2096,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.5"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Accurate and complete mapping of short-read sequencing to a reference genome greatly enhances the discovery of biological results and improves statistical predictions. We recently presented RNA-MATE, a pipeline for the recursive mapping of RNA-Seq datasets. With the rapid increase in genome re-sequencing projects, progression of available mapping software and the evolution of file formats, we now present X-MATE, an updated version of RNA-MATE, capable of mapping both RNA-Seq and DNA datasets and with improved performance, output file formats, configuration files, and flexibility in core mapping software.<\/jats:p>\n               <jats:p>Availability: Executables, source code, junction libraries, test data and results and the user manual are available from http:\/\/grimmond.imb.uq.edu.au\/X-MATE\/.<\/jats:p>\n               <jats:p>Contact: \u00a0n.cloonan@uq.edu.au; s.grimmond@uq.edu.au<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics Online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq698","type":"journal-article","created":{"date-parts":[[2011,1,8]],"date-time":"2011-01-08T01:26:38Z","timestamp":1294449998000},"page":"580-581","source":"Crossref","is-referenced-by-count":10,"title":["X-MATE: a flexible system for mapping short read data"],"prefix":"10.1093","volume":"27","author":[{"given":"David L. A.","family":"Wood","sequence":"first","affiliation":[{"name":"Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St. Lucia 4072, Queensland, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qinying","family":"Xu","sequence":"additional","affiliation":[{"name":"Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St. Lucia 4072, Queensland, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John V.","family":"Pearson","sequence":"additional","affiliation":[{"name":"Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St. Lucia 4072, Queensland, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nicole","family":"Cloonan","sequence":"additional","affiliation":[{"name":"Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St. Lucia 4072, Queensland, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sean M.","family":"Grimmond","sequence":"additional","affiliation":[{"name":"Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St. Lucia 4072, Queensland, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2011,1,6]]},"reference":[{"key":"2023012511575109000_B1","doi-asserted-by":"crossref","first-page":"2615","DOI":"10.1093\/bioinformatics\/btp459","article-title":"RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data","volume":"25","author":"Cloonan","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012511575109000_B2","doi-asserted-by":"crossref","first-page":"R86","DOI":"10.1186\/gb-2010-11-8-r86","article-title":"Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences","volume":"11","author":"Goecks","year":"2010","journal-title":"Genome Biol."},{"key":"2023012511575109000_B3","doi-asserted-by":"crossref","first-page":"2613","DOI":"10.1093\/bioinformatics\/btp438","article-title":"Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite","volume":"25","author":"Hashimoto","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012511575109000_B4","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1101\/gr.229102","article-title":"The human genome browser at UCSC","volume":"12","author":"Kent","year":"2002","journal-title":"Genome Res."},{"key":"2023012511575109000_B5","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012511575109000_B6","doi-asserted-by":"crossref","first-page":"S22","DOI":"10.1038\/nmeth.1371","article-title":"Computation for ChIP-seq and RNA-seq studies","volume":"6","author":"Pepke","year":"2009","journal-title":"Nature. 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Biotechnol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/4\/580\/48866854\/bioinformatics_27_4_580.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/4\/580\/48866854\/bioinformatics_27_4_580.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T12:47:04Z","timestamp":1674650824000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/4\/580\/198439"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,1,6]]},"references-count":7,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2011,2,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq698","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,2,15]]},"published":{"date-parts":[[2011,1,6]]}}}