{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T21:50:50Z","timestamp":1774389050736,"version":"3.50.1"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The significance and function of posttranscriptional cytosine methylation in poly(A)RNA attracts great interest but is still poorly understood. High-throughput sequencing of RNA treated with bisulfite (RNA-BSseq) or subjected to enrichment techniques like Aza-IP or miCLIP enables transcriptome wide studies of this particular modification at single base pair resolution. However, to date, there are no specialized software tools available for the analysis of RNA-BSseq or Aza-IP data. Therefore, we developed meRanTK, the first publicly available tool kit which addresses the special demands of high-throughput RNA cytosine methylation data analysis. It provides fast and easy to use splice-aware bisulfite sequencing read mapping, comprehensive methylation calling and identification of differentially methylated cytosines by statistical analysis of single- and multi-replicate experiments. Application of meRanTK to RNA-BSseq or Aza-IP data produces accurate results in standard compliant formats.<\/jats:p>\n               <jats:p>Availability and Implementation: meRanTK, source code and test data are released under the GNU GPLv3+ license and are available at http:\/\/icbi.at\/software\/meRanTK\/.<\/jats:p>\n               <jats:p>Contact: \u00a0dietmar.rieder@i-med.ac.at<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv647","type":"journal-article","created":{"date-parts":[[2015,11,6]],"date-time":"2015-11-06T01:34:15Z","timestamp":1446773655000},"page":"782-785","source":"Crossref","is-referenced-by-count":69,"title":["meRanTK: methylated RNA analysis ToolKit"],"prefix":"10.1093","volume":"32","author":[{"given":"Dietmar","family":"Rieder","sequence":"first","affiliation":[{"name":"1 Division of Bioinformatics and"}]},{"given":"Thomas","family":"Amort","sequence":"additional","affiliation":[{"name":"2 Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria"}]},{"given":"Elisabeth","family":"Kugler","sequence":"additional","affiliation":[{"name":"1 Division of Bioinformatics and"}]},{"given":"Alexandra","family":"Lusser","sequence":"additional","affiliation":[{"name":"2 Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria"}]},{"given":"Zlatko","family":"Trajanoski","sequence":"additional","affiliation":[{"name":"1 Division of Bioinformatics and"}]}],"member":"286","published-online":{"date-parts":[[2015,11,4]]},"reference":[{"key":"2023020110450213700_btv647-B1","doi-asserted-by":"crossref","first-page":"1003","DOI":"10.4161\/rna.24454","article-title":"Long non-coding RNAs as targets for cytosine methylation","volume":"10","author":"Amort","year":"2013","journal-title":"RNA Biol."},{"key":"2023020110450213700_btv647-B2","doi-asserted-by":"crossref","first-page":"217","DOI":"10.12688\/f1000research.2-217.v1","article-title":"MethylExtract: high-quality methylation maps and SNV calling from whole genome bisulfite sequencing data","volume":"2","author":"Barturen","year":"2013","journal-title":"F1000Research"},{"key":"2023020110450213700_btv647-B3","doi-asserted-by":"crossref","first-page":"D195","DOI":"10.1093\/nar\/gkq1028","article-title":"The RNA modification database, RNAMDB: 2011 update","volume":"39","author":"Cantara","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023020110450213700_btv647-B4","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"2023020110450213700_btv647-B5","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1016\/j.celrep.2013.06.029","article-title":"NSun2-mediated cytosine-5 methylation of vault noncoding RNA determines its processing into regulatory small RNAs","volume":"4","author":"Hussain","year":"2013","journal-title":"Cell Rep."},{"key":"2023020110450213700_btv647-B6","doi-asserted-by":"crossref","first-page":"458","DOI":"10.1038\/nbt.2566","article-title":"Identification of direct targets and modified bases of RNA cytosine methyltransferases","volume":"31","author":"Khoddami","year":"2013","journal-title":"Nat. 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