{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,28]],"date-time":"2026-03-28T03:55:56Z","timestamp":1774670156921,"version":"3.50.1"},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2016,11,16]],"date-time":"2016-11-16T00:00:00Z","timestamp":1479254400000},"content-version":"vor","delay-in-days":90,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"FKZ","award":["031A533"],"award-info":[{"award-number":["031A533"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,12,15]]},"abstract":"<jats:p>Motivation: The vast amount of already available and currently generated read mapping data requires comprehensive visualization, and should benefit from bioinformatics tools offering a wide spectrum of analysis functionality from just one source. Appropriate handling of multiple mapped reads during mapping analyses remains an issue that demands improvement.<\/jats:p>\n               <jats:p>Results: The capabilities of the read mapping analysis and visualization tool ReadXplorer were vastly enhanced. Here, we present an even finer granulated read mapping classification, improving the level of detail for analyses and visualizations. The spectrum of automatic analysis functions has been broadened to include genome rearrangement detection as well as correlation analysis between two mapping data sets. Existing functions were refined and enhanced, namely the computation of differentially expressed genes, the read count and normalization analysis and the transcription start site detection. Additionally, ReadXplorer 2 features a highly improved support for large eukaryotic data sets and a command line version, enabling its integration into workflows. Finally, the new version is now able to display any kind of tabular results from other bioinformatics tools.<\/jats:p>\n               <jats:p>Availability and Implementation: \u00a0http:\/\/www.readxplorer.org<\/jats:p>\n               <jats:p>Contact: \u00a0readxplorer@computational.bio.uni-giessen.de<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw541","type":"journal-article","created":{"date-parts":[[2016,8,19]],"date-time":"2016-08-19T01:19:13Z","timestamp":1471569553000},"page":"3702-3708","source":"Crossref","is-referenced-by-count":81,"title":["ReadXplorer 2\u2014detailed read mapping analysis and visualization from one single source"],"prefix":"10.1093","volume":"32","author":[{"given":"Rolf","family":"Hilker","sequence":"first","affiliation":[{"name":"1Bioinformatics and Systems Biology, Faculty of Biology and Chemistry, Justus-Liebig-University, Giessen 35392, Germany"}]},{"given":"Kai Bernd","family":"Stadermann","sequence":"additional","affiliation":[{"name":"2Faculty of Biology, Chair of Genome Research, Bielefeld University, Bielefeld 33615, Germany"}]},{"given":"Oliver","family":"Schwengers","sequence":"additional","affiliation":[{"name":"1Bioinformatics and Systems Biology, Faculty of Biology and Chemistry, Justus-Liebig-University, Giessen 35392, Germany"}]},{"given":"Evgeny","family":"Anisiforov","sequence":"additional","affiliation":[{"name":"1Bioinformatics and Systems Biology, Faculty of Biology and Chemistry, Justus-Liebig-University, Giessen 35392, Germany"}]},{"given":"Sebastian","family":"Jaenicke","sequence":"additional","affiliation":[{"name":"1Bioinformatics and Systems Biology, Faculty of Biology and Chemistry, Justus-Liebig-University, Giessen 35392, Germany"}]},{"given":"Bernd","family":"Weisshaar","sequence":"additional","affiliation":[{"name":"2Faculty of Biology, Chair of Genome Research, Bielefeld University, Bielefeld 33615, Germany"}]},{"given":"Tobias","family":"Zimmermann","sequence":"additional","affiliation":[{"name":"1Bioinformatics and Systems Biology, Faculty of Biology and Chemistry, Justus-Liebig-University, Giessen 35392, Germany"}]},{"given":"Alexander","family":"Goesmann","sequence":"additional","affiliation":[{"name":"1Bioinformatics and Systems Biology, Faculty of Biology and Chemistry, Justus-Liebig-University, Giessen 35392, Germany"}]}],"member":"286","published-online":{"date-parts":[[2016,8,18]]},"reference":[{"key":"2023020114080661500_btw541-B1","doi-asserted-by":"crossref","first-page":"e12\u2013e12","DOI":"10.1093\/nar\/gkr995","article-title":"GenomeView: a next-generation genome browser","volume":"40","author":"Abeel","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2023020114080661500_btw541-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":"2023020114080661500_btw541-B3","doi-asserted-by":"crossref","first-page":"R106.","DOI":"10.1186\/gb-2010-11-10-r106","article-title":"Differential expression analysis for sequence count data","volume":"11","author":"Anders","year":"2010","journal-title":"Genome Biol"},{"key":"2023020114080661500_btw541-B36","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","article-title":"HTSeqa Python framework to work with high-throughput sequencing data","volume":"31","author":"Anders","year":"2015","journal-title":"Bioinformatics"},{"key":"2023020114080661500_btw541-B4","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1038\/nature07517","article-title":"Accurate whole human genome sequencing using reversible terminator chemistry","volume":"456","author":"Bentley","year":"2008","journal-title":"Nature"},{"key":"2023020114080661500_btw541-B5","doi-asserted-by":"crossref","first-page":"783","DOI":"10.1128\/CMR.00003-14","article-title":"Emerging Technologies for the Clinical Microbiology Laboratory","volume":"27","author":"Buchan","year":"2014","journal-title":"Clin. 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