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Nucleic Acids Res. 2014 Jul;42(Web Server issue):W187-91. doi: 10.1093/nar/gku365. Epub 2014 May 5.

deepTools: a flexible platform for exploring deep-sequencing data.

Author information

1
Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany.
2
Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany.
3
Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, Germany.
4
Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany manke@ie-freiburg.mpg.de.

Abstract

We present a Galaxy based web server for processing and visualizing deeply sequenced data. The web server's core functionality consists of a suite of newly developed tools, called deepTools, that enable users with little bioinformatic background to explore the results of their sequencing experiments in a standardized setting. Users can upload pre-processed files with continuous data in standard formats and generate heatmaps and summary plots in a straight-forward, yet highly customizable manner. In addition, we offer several tools for the analysis of files containing aligned reads and enable efficient and reproducible generation of normalized coverage files. As a modular and open-source platform, deepTools can easily be expanded and customized to future demands and developments. The deepTools webserver is freely available at http://deeptools.ie-freiburg.mpg.de and is accompanied by extensive documentation and tutorials aimed at conveying the principles of deep-sequencing data analysis. The web server can be used without registration. deepTools can be installed locally either stand-alone or as part of Galaxy.

PMID:
24799436
PMCID:
PMC4086134
DOI:
10.1093/nar/gku365
[Indexed for MEDLINE]
Free PMC Article

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