title: meRanTK: methylated RNA analysis ToolKit.
abstract: 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.
  
  
  
  meRanTK, source code and test data are released under the GNU GPLv3+ license and are available at http://icbi.at/software/meRanTK/ CONTACT: dietmar.rieder@i-med.ac.at.
authors.affiliation: Division of Bioinformatics and.
authors.forename: Dietmar
authors.initials: D
authors.lastname: Rieder
authors.affiliation: Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria.
authors.forename: Thomas
authors.initials: T
authors.lastname: Amort
authors.affiliation: Division of Bioinformatics and.
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Kugler
authors.affiliation: Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Lusser
authors.affiliation: Division of Bioinformatics and.
authors.forename: Zlatko
authors.initials: Z
authors.lastname: Trajanoski
mesh_terms: D003596:Cytosine; D019175:DNA Methylation; D012313:RNA; D017422:Sequence Analysis, DNA; D012984:Software; D059467:Transcriptome
chemical_list: D012313:RNA; D003596:Cytosine