{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:57Z","timestamp":1772138097381,"version":"3.50.1"},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2019,8,16]],"date-time":"2019-08-16T00:00:00Z","timestamp":1565913600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Standard bioinformatics pipelines for the analysis of bacterial transcriptomic data commonly ignore non-coding but functional elements e.g. small RNAs, long antisense RNAs or untranslated regions (UTRs) of mRNA transcripts. The root of this problem is the use of incomplete genome annotation files. Here, we present baerhunter, a coverage-based method implemented in R, that automates the discovery of expressed non-coding RNAs and UTRs from RNA-seq reads mapped to a reference genome. The core algorithm is part of a pipeline that facilitates downstream analysis of both coding and non-coding features. The method is simple, easy to extend and customize and, in limited tests with simulated and real data, compares favourably against the currently most popular alternative.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The baerhunter R package is available from: https:\/\/github.com\/irilenia\/baerhunter<\/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\/btz643","type":"journal-article","created":{"date-parts":[[2019,8,13]],"date-time":"2019-08-13T07:26:39Z","timestamp":1565681199000},"page":"966-969","source":"Crossref","is-referenced-by-count":10,"title":["baerhunter: an\n                    <i>R<\/i>\n                    package for the discovery and analysis of expressed non-coding regions in bacterial RNA-seq data"],"prefix":"10.1093","volume":"36","author":[{"given":"A","family":"Ozuna","sequence":"first","affiliation":[{"name":"Department of Biological Sciences, Institute of Structural and Molecular Biology , London, WC1E 7HX, UK"}]},{"given":"D","family":"Liberto","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Institute of Structural and Molecular Biology , London, WC1E 7HX, UK"}]},{"given":"R M","family":"Joyce","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Institute of Structural and Molecular Biology , London, WC1E 7HX, UK"}]},{"given":"K B","family":"Arnvig","sequence":"additional","affiliation":[{"name":"Institute of Structural and Molecular Biology, Division of Biosciences, University College London , London, WC1E 6BT, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8616-170X","authenticated-orcid":false,"given":"I","family":"Nobeli","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Institute of Structural and Molecular Biology , London, WC1E 7HX, UK"}]}],"member":"286","published-online":{"date-parts":[[2019,8,16]]},"reference":[{"key":"2023013110092669600_btz643-B1","doi-asserted-by":"crossref","first-page":"W537","DOI":"10.1093\/nar\/gky379","article-title":"The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update","volume":"46","author":"Afgan","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023013110092669600_btz643-B2","doi-asserted-by":"crossref","first-page":"89.","DOI":"10.1186\/1471-2105-15-89","article-title":"TSSAR: TSS annotation regime for dRNA-seq data","volume":"15","author":"Amman","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"2023013110092669600_btz643-B3","doi-asserted-by":"crossref","first-page":"e1002342.","DOI":"10.1371\/journal.ppat.1002342","article-title":"Sequence-based analysis uncovers an abundance of non-coding RNA in the total transcriptome of Mycobacterium tuberculosis","volume":"7","author":"Arnvig","year":"2011","journal-title":"PLoS Pathogens"},{"key":"2023013110092669600_btz643-B4","doi-asserted-by":"crossref","first-page":"464","DOI":"10.1093\/bioinformatics\/btr703","article-title":"Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data","volume":"28","author":"Carver","year":"2012","journal-title":"Bioinformatics"},{"key":"2023013110092669600_btz643-B5","doi-asserted-by":"crossref","first-page":"1121","DOI":"10.1016\/j.celrep.2013.10.031","article-title":"Genome-wide mapping of transcriptional start sites defines an extensive leaderless transcriptome in Mycobacterium tuberculosis","volume":"5","author":"Cortes","year":"2013","journal-title":"Cell Rep"},{"key":"2023013110092669600_btz643-B6","doi-asserted-by":"crossref","first-page":"2778","DOI":"10.1093\/bioinformatics\/btv272","article-title":"Polyester: simulating RNA-seq datasets with differential transcript expression","volume":"31","author":"Frazee","year":"2015","journal-title":"Bioinformatics"},{"key":"2023013110092669600_btz643-B7","doi-asserted-by":"crossref","DOI":"10.3389\/fcimb.2014.00096","article-title":"Small RNAs in mycobacteria: an unfolding story","volume":"4","author":"Haning","year":"2014","journal-title":"Front. 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