title: ReadXplorer 2-detailed read mapping analysis and visualization from one single source.
abstract: 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.
  
  
  
  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.
  
  
  
  http://www.readxplorer.org CONTACT: readxplorer@computational.bio.uni-giessen.deSupplementary information: Supplementary data are available at Bioinformatics online.
authors.affiliation: Bioinformatics and Systems Biology, Faculty of Biology and Chemistry, Justus-Liebig-University, Giessen 35392, Germany.
authors.forename: Rolf
authors.initials: R
authors.lastname: Hilker
authors.affiliation: Faculty of Biology, Chair of Genome Research, Bielefeld University, Bielefeld 33615, Germany.
authors.forename: Kai Bernd
authors.initials: KB
authors.lastname: Stadermann
authors.affiliation: Bioinformatics and Systems Biology, Faculty of Biology and Chemistry, Justus-Liebig-University, Giessen 35392, Germany.
authors.forename: Oliver
authors.initials: O
authors.lastname: Schwengers
authors.affiliation: Bioinformatics and Systems Biology, Faculty of Biology and Chemistry, Justus-Liebig-University, Giessen 35392, Germany.
authors.forename: Evgeny
authors.initials: E
authors.lastname: Anisiforov
authors.affiliation: Bioinformatics and Systems Biology, Faculty of Biology and Chemistry, Justus-Liebig-University, Giessen 35392, Germany.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Jaenicke
authors.affiliation: Faculty of Biology, Chair of Genome Research, Bielefeld University, Bielefeld 33615, Germany.
authors.forename: Bernd
authors.initials: B
authors.lastname: Weisshaar
authors.affiliation: Bioinformatics and Systems Biology, Faculty of Biology and Chemistry, Justus-Liebig-University, Giessen 35392, Germany.
authors.forename: Tobias
authors.initials: T
authors.lastname: Zimmermann
authors.affiliation: Bioinformatics and Systems Biology, Faculty of Biology and Chemistry, Justus-Liebig-University, Giessen 35392, Germany.
authors.forename: Alexander
authors.initials: A
authors.lastname: Goesmann
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D015870:Gene Expression; D016678:Genome; D056914:Genomic Structural Variation; D018749:RNA, Plant / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D024363:Transcription Initiation Site
chemical_list: D018749:RNA, Plant