Web-based analysis of (Epi-) genome data using EpiGRAPH and galaxy

Christoph Bock, Greg Von Kuster, Konstantin Halachev, James Taylor, Anton Nekrutenko, Thomas Lengauer

Research output: Chapter in Book/Report/Conference proceedingChapter

10 Scopus citations

Abstract

Modern life sciences are becoming increasingly data intensive, posing a significant challenge for most researchers and shifting the bottleneck of scientific discovery from data generation to data analysis. As a result, progress in genome research is increasingly impeded by bioinformatic hurdles. A new generation of powerful and easy-to-use genome analysis tools has been developed to address this issue, enabling biologists to perform complex bioinformatic analyses online - without having to learn a programming language or downloading and manually processing large datasets. In this tutorial paper, we describe the use of EpiGRAPH (http://epigraph.mpi-inf.mpg.de/) and Galaxy (http://galaxyproject.org/) for genome and epigenome analysis, and we illustrate how these two web services work together to identify epigenetic modifications that are characteristics of highly polymorphic (SNP-rich) promoters. This paper is supplemented with video tutorials (http://tinyurl.com/yc5xkqq), which provide a step-by-step guide through each example analysis.

Original languageEnglish (US)
Title of host publicationGenetic Variation
Subtitle of host publicationMethods and Protocols
PublisherHumana Press Inc.
Pages275-296
Number of pages22
ISBN (Print)9781603273664
DOIs
StatePublished - 2010

Publication series

NameMethods in Molecular Biology
Volume628
ISSN (Print)1064-3745

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics

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