• The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy

    • Björn A. Grüning
      Bioinformatics Group, Department of Computer Science, University of Freiburg
    • Jörg Fallmann
      Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig
    • Dilmurat Yusuf
      Berlin Institute for Medical Systems Biology
    • Sebastian Will
      Institut für Theoretische Chemie, Fakultät für Chemie, Universität Wien
    • Anika Erxleben
      Bioinformatics Group, Department of Computer Science, University of Freiburg
    • Florian Eggenhofer
      Bioinformatics Group, Department of Computer Science, University of Freiburg
    • Torsten Houwaart
      Bioinformatics Group, Department of Computer Science, University of Freiburg
    • Bérénice Batut
      Bioinformatics Group, Department of Computer Science, University of Freiburg
    • Pavankumar Videm
      Bioinformatics Group, Department of Computer Science, University of Freiburg
    • Andrea Bagnacani
      Department of Systems Biology and Bioinformatics, University of Rostock
    • Markus Wolfien
      Department of Systems Biology and Bioinformatics, University of Rostock
    • Steffen C. Lott
      Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg
    • Youri Hoogstrate
      Department of Urology, Erasmus University Medical Center
    • Wolfgang R. Hess
      Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg
    • Olaf Wolkenhauer
      Department of Systems Biology and Bioinformatics, University of Rostock
    • Steve Hoffmann
      Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig
    • Altuna Akalin
      Berlin Institute for Medical Systems Biology
    • Uwe Ohler
      Berlin Institute for Medical Systems Biology
    • Peter F. Stadler
      Institut für Theoretische Chemie, Fakultät für Chemie, Universität Wien
    • Rolf Backofen
      Bioinformatics Group, Department of Computer Science, University of Freiburg
  • RNA-based regulation has become a major research topic in molecular biology. The analysis of epigenetic and expression data is therefore incomplete if RNA-based regulation is not taken into account. Thus, it is increasingly important but not yet standard to combine RNA-centric data and analysis tools with other types of experimental data such as RNA-seq or ChIP-seq. Here, we present the RNA workbench, a comprehensive set of analysis tools and consolidated workflows that enable the researcher to combine these two worlds. Based on the Galaxy framework the workbench guarantees simple access, easy extension, flexible adaption to personal and security needs, and sophisticated analyses that are independent of command-line knowledge. Currently, it includes more than 50 bioinformatics tools that are dedicated to different research areas of RNA biology including RNA structure analysis, RNA alignment, RNA annotation, RNA-protein interaction, ribosome profiling, RNA-seq analysis and RNA target prediction. The workbench is developed and maintained by experts in RNA bioinformatics and the Galaxy framework. Together with the growing community evolving around this workbench, we are committed to keep the workbench up-to-date for future standards and needs, providing researchers with a reliable and robust framework for RNA data analysis. Availability: The RNA workbench is available at https://github.com/bgruening/galaxy-rna-workbench.

  • PDF

  • http://phaidra.univie.ac.at/o:907611

  • Wissenschaftlicher Artikel

  • Veröffentlichte Version

  • Nucleic Acids Research

  • 2017

  • 45

  • W1

  • Oxford University Press (OUP)

  • Englisch

  • Frei zugänglich

  • 0305-1048