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 Citations (Scopus)

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 - Jan 1 2010

Publication series

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

Fingerprint

Galaxies
Genome
Computational Biology
Programming Languages
Biological Science Disciplines
Epigenomics
Single Nucleotide Polymorphism
Research Personnel
Research

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics

Cite this

Bock, C., Von Kuster, G., Halachev, K., Taylor, J., Nekrutenko, A., & Lengauer, T. (2010). Web-based analysis of (Epi-) genome data using EpiGRAPH and galaxy. In Genetic Variation: Methods and Protocols (pp. 275-296). (Methods in Molecular Biology; Vol. 628). Humana Press Inc.. https://doi.org/10.1007/978-1-60327-367-1_15
Bock, Christoph ; Von Kuster, Greg ; Halachev, Konstantin ; Taylor, James ; Nekrutenko, Anton ; Lengauer, Thomas. / Web-based analysis of (Epi-) genome data using EpiGRAPH and galaxy. Genetic Variation: Methods and Protocols. Humana Press Inc., 2010. pp. 275-296 (Methods in Molecular Biology).
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Bock, C, Von Kuster, G, Halachev, K, Taylor, J, Nekrutenko, A & Lengauer, T 2010, Web-based analysis of (Epi-) genome data using EpiGRAPH and galaxy. in Genetic Variation: Methods and Protocols. Methods in Molecular Biology, vol. 628, Humana Press Inc., pp. 275-296. https://doi.org/10.1007/978-1-60327-367-1_15

Web-based analysis of (Epi-) genome data using EpiGRAPH and galaxy. / Bock, Christoph; Von Kuster, Greg; Halachev, Konstantin; Taylor, James; Nekrutenko, Anton; Lengauer, Thomas.

Genetic Variation: Methods and Protocols. Humana Press Inc., 2010. p. 275-296 (Methods in Molecular Biology; Vol. 628).

Research output: Chapter in Book/Report/Conference proceedingChapter

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Bock C, Von Kuster G, Halachev K, Taylor J, Nekrutenko A, Lengauer T. Web-based analysis of (Epi-) genome data using EpiGRAPH and galaxy. In Genetic Variation: Methods and Protocols. Humana Press Inc. 2010. p. 275-296. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-60327-367-1_15