{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,14]],"date-time":"2026-03-14T08:10:40Z","timestamp":1773475840937,"version":"3.50.1"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"23","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Summary: RNA-Seq has become a potent and widely used method to qualitatively and quantitatively study transcriptomes. To draw biological conclusions based on RNA-Seq data, several steps, some of which are computationally intensive, have to be taken. Our READemption pipeline takes care of these individual tasks and integrates them into an easy-to-use tool with a command line interface. To leverage the full power of modern computers, most subcommands of READemption offer parallel data processing. While READemption was mainly developed for the analysis of bacterial primary transcriptomes, we have successfully applied it to analyze RNA-Seq reads from other sample types, including whole transcriptomes and RNA immunoprecipitated with proteins, not only from bacteria but also from eukaryotes and archaea.<\/jats:p>\n                  <jats:p>Availability and implementation: READemption is implemented in Python and is published under the ISC open source license. The tool and documentation is hosted at http:\/\/pythonhosted.org\/READemption (DOI:10.6084\/m9.figshare.977849).<\/jats:p>\n                  <jats:p>Contact: \u00a0cynthia.sharma@uni-wuerzburg.de and konrad.foerstner@uni-wuerzburg.de<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu533","type":"journal-article","created":{"date-parts":[[2014,8,15]],"date-time":"2014-08-15T01:12:51Z","timestamp":1408065171000},"page":"3421-3423","source":"Crossref","is-referenced-by-count":173,"title":["READemption\u2014a tool for the computational analysis of deep-sequencing\u2013based transcriptome data"],"prefix":"10.1093","volume":"30","author":[{"given":"Konrad U.","family":"F\u00f6rstner","sequence":"first","affiliation":[{"name":"Institute for Molecular Infection Biology 1 \u00a0 and 2 , , D-97080 W\u00fcrzburg, Germany"},{"name":"Research Centre for Infectious Diseases (ZINF) 1 \u00a0 and 2 , , D-97080 W\u00fcrzburg, Germany"},{"name":"University of W\u00fcrzburg 1 \u00a0 and 2 , , D-97080 W\u00fcrzburg, Germany"},{"name":"Institute for Molecular Infection Biology 1 \u00a0 and 2 , , D-97080 W\u00fcrzburg, Germany"},{"name":"Research Centre for Infectious Diseases (ZINF) 1 \u00a0 and 2 , , D-97080 W\u00fcrzburg, Germany"},{"name":"University of W\u00fcrzburg 1 \u00a0 and 2 , , D-97080 W\u00fcrzburg, Germany"}]},{"given":"J\u00f6rg","family":"Vogel","sequence":"additional","affiliation":[{"name":"Institute for Molecular Infection Biology 1 \u00a0 and 2 , , D-97080 W\u00fcrzburg, Germany"},{"name":"Research Centre for Infectious Diseases (ZINF) 1 \u00a0 and 2 , , D-97080 W\u00fcrzburg, Germany"},{"name":"University of W\u00fcrzburg 1 \u00a0 and 2 , , D-97080 W\u00fcrzburg, Germany"}]},{"given":"Cynthia M.","family":"Sharma","sequence":"additional","affiliation":[{"name":"Institute for Molecular Infection Biology 1 \u00a0 and 2 , , D-97080 W\u00fcrzburg, Germany"},{"name":"Research Centre for Infectious Diseases (ZINF) 1 \u00a0 and 2 , , D-97080 W\u00fcrzburg, Germany"},{"name":"University of W\u00fcrzburg 1 \u00a0 and 2 , , D-97080 W\u00fcrzburg, Germany"}]}],"member":"286","published-online":{"date-parts":[[2014,8,13]]},"reference":[{"key":"2023012712041385800_btu533-B1","doi-asserted-by":"crossref","first-page":"R10","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":"2023012712041385800_btu533-B2","doi-asserted-by":"crossref","first-page":"1422","DOI":"10.1093\/bioinformatics\/btp163","article-title":"Biopython: freely available Python tools for computational molecular biology and bioinformatics","volume":"25","author":"Cock","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012712041385800_btu533-B3","doi-asserted-by":"crossref","first-page":"2532","DOI":"10.1093\/bioinformatics\/bts477","article-title":"easyRNASeq: a bioconductor package for processing RNA-Seq data","volume":"28","author":"Delhomme","year":"2012","journal-title":"Bioinformatics"},{"key":"2023012712041385800_btu533-B4","doi-asserted-by":"crossref","first-page":"e1003495","DOI":"10.1371\/journal.pgen.1003495","article-title":"High-resolution transcriptome maps reveal strain-specific regulatory features of multiple Campylobacter jejuni isolates","volume":"9","author":"Dugar","year":"2013","journal-title":"PLoS Genet."},{"key":"2023012712041385800_btu533-B5","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1016\/j.mib.2011.07.023","article-title":"Progress in prokaryotic transcriptomics","volume":"14","author":"Filiatrault","year":"2011","journal-title":"Curr. 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