{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T04:39:34Z","timestamp":1775623174753,"version":"3.50.1"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"23","license":[{"start":{"date-parts":[[2019,5,29]],"date-time":"2019-05-29T00:00:00Z","timestamp":1559088000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000038","name":"NSERC","doi-asserted-by":"publisher","award":["RGPIN-2018-05412"],"award-info":[{"award-number":["RGPIN-2018-05412"]}],"id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Canada Research Chair in RNA Biology and Cancer Genomics"},{"name":"Fonds de Recherche du Qu\u00e9bec Sant\u00e9"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Next-generation sequencing techniques revolutionized the study of RNA expression by permitting whole transcriptome analysis. However, sequencing reads generated from nested and multi-copy genes are often either misassigned or discarded, which greatly reduces both quantification accuracy and gene coverage.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here we present count corrector (CoCo), a read assignment pipeline that takes into account the multitude of overlapping and repetitive genes in the transcriptome of higher eukaryotes. CoCo uses a modified annotation file that highlights nested genes and proportionally distributes multimapped reads between repeated sequences. CoCo salvages over 15% of discarded aligned RNA-seq reads and significantly changes the abundance estimates for both coding and non-coding RNA as validated by PCR and bedgraph comparisons.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The CoCo software is an open source package written in Python and available from http:\/\/gitlabscottgroup.med.usherbrooke.ca\/scott-group\/coco.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz433","type":"journal-article","created":{"date-parts":[[2019,5,24]],"date-time":"2019-05-24T15:12:03Z","timestamp":1558710723000},"page":"5039-5047","source":"Crossref","is-referenced-by-count":37,"title":["CoCo: RNA-seq read assignment correction for nested genes and multimapped reads"],"prefix":"10.1093","volume":"35","author":[{"given":"Gabrielle","family":"Deschamps-Francoeur","sequence":"first","affiliation":[{"name":"Department of Biochemistry and RNA Group, Universit\u00e9 de Sherbrooke, Sherbrooke , QC, Canada"}]},{"given":"Vincent","family":"Boivin","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and RNA Group, Universit\u00e9 de Sherbrooke, Sherbrooke , QC, Canada"}]},{"given":"Sherif","family":"Abou Elela","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Sherbrooke Department of Microbiology and Infectiology, Faculty of Medicine and Health Sciences, , Sherbrooke, QC, Canada"}]},{"given":"Michelle S","family":"Scott","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and RNA Group, Universit\u00e9 de Sherbrooke, Sherbrooke , QC, Canada"}]}],"member":"286","published-online":{"date-parts":[[2019,5,29]]},"reference":[{"key":"2023013108325565700_btz433-B1","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","article-title":"HTSeq\u2013a Python framework to work with high-throughput sequencing data","volume":"31","author":"Anders","year":"2015","journal-title":"Bioinformatics"},{"key":"2023013108325565700_btz433-B2","doi-asserted-by":"crossref","first-page":"950","DOI":"10.1261\/rna.064493.117","article-title":"Simultaneous sequencing of coding and noncoding RNA reveals a human transcriptome dominated by a small number of highly expressed noncoding genes","volume":"24","author":"Boivin","year":"2018","journal-title":"RNA"},{"key":"2023013108325565700_btz433-B3","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/j.semcdb.2017.08.016","article-title":"Protein coding genes as hosts for noncoding RNA expression","volume":"75","author":"Boivin","year":"2018","journal-title":"Semin. 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