{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T00:35:58Z","timestamp":1773275758417,"version":"3.50.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2016,10,1]],"date-time":"2016-10-01T00:00:00Z","timestamp":1475280000000},"content-version":"vor","delay-in-days":2620,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Mapping of next-generation sequencing data derived from RNA samples (RNAseq) presents different genome mapping challenges than data derived from DNA. For example, tags that cross exon-junction boundaries will often not map to a reference genome, and the strand specificity of the data needs to be retained. Here we present RNA-MATE, a computational pipeline based on a recursive mapping strategy for placing strand specific RNAseq data onto a reference genome. Maximizing the mappable tags can provide significant savings in the cost of sequencing experiments. This pipeline provides an automatic and integrated way to align color-space sequencing data, collate this information and generate files for examining gene-expression data in a genomic context.<\/jats:p>\n               <jats:p>Availability: Executables, source code, and exon-junction libraries are available from http:\/\/grimmond.imb.uq.edu.au\/RNA-MATE\/<\/jats:p>\n               <jats:p>Contact: \u00a0n.cloonan@imb.uq.edu.au<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics Online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp459","type":"journal-article","created":{"date-parts":[[2009,8,1]],"date-time":"2009-08-01T00:14:58Z","timestamp":1249085698000},"page":"2615-2616","source":"Crossref","is-referenced-by-count":38,"title":["RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data"],"prefix":"10.1093","volume":"25","author":[{"given":"Nicole","family":"Cloonan","sequence":"first","affiliation":[{"name":"Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St. Lucia 4072, 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, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Geoffrey J.","family":"Faulkner","sequence":"additional","affiliation":[{"name":"Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St. Lucia 4072, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Darrin F.","family":"Taylor","sequence":"additional","affiliation":[{"name":"Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St. Lucia 4072, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dave T. P.","family":"Tang","sequence":"additional","affiliation":[{"name":"Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St. Lucia 4072, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gabriel","family":"Kolle","sequence":"additional","affiliation":[{"name":"Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St. Lucia 4072, 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, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2009,7,30]]},"reference":[{"key":"2023013112125515000_B1","doi-asserted-by":"crossref","first-page":"626","DOI":"10.1038\/ng1789","article-title":"Genome-wide analysis of mammalian promoter architecture and evolution","volume":"38","author":"Carninci","year":"2006","journal-title":"Nat. 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