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EpiCenter

Overview

EpiCenter is a powerful analysis tool of genome-wide mRNA-seq or ChIP-seq data for detecting differentially expressed genes or identifying changes in epigenetic modifications (histone acetylation/methylation patterns). EpiCenter is also capable of performing genome-wide TFBS peaking detection and generating read coverage depth plot data (e.g., WIG files for UCSC genome browser). Implemented with C++ language, EpiCenter is efficient, and typically requires less than 10 minutes to analyze a large dataset. EpiCenter supports major read alignment formats including SAM, BAM, ELAND export, MAQ, and UCSC BED file formats. For our detailed methods, please see our publication on NAR



  Epicenter output sample plot  

Citation

W Huang, DM Umbach, N Vincent Jordan, AN Abell, GL Johnson, and L Li. Efficiently identifying genome-wide changes with next-generation sequencing data. Nucl. Acids Res. (2011) [Abstract]


Availability

EpiCenter is freely available to the public. The binary packages of EpiCenter are available for all three major operating systems: Linux, Macintosh, and Windows, and can be downloaded at the following links. The C++ source code is also available upon request for advanced users.

NOTE: please install and use a 64-bit version program if you have 64-bit operating system. 32 bit packages are for the 32-bit operating system and you may be not able to use it to analyze very large datasets if more than 4GB memory is required for the analysis.


Download

Version 1-7-0-8 (Latest Version)

Version 1-6-1-8

Version 1-5-9-8

Version 1-5-8-8

Version 1-5-7-8


Installation

Recommended hardware requirements:

  • CPU: 1GHZ or higher
  • Memory: 4GB or more
  • Disk space: 100GB or more

Installation is to simply decompress one of the above EpiCenter compressed packages to your installation location.

Linux or MacOS X

If you download the package epicenter_<OS>.tar.gz to the folder "/home/<username>/downloads", and then you can issue the following commands to install the program to the folder "/home/<username>/install_dir" at your terminal window:

  • cd /home/<username>/install_dir
  • tar xfz /home/<username>/downloads/epicenter_<OS>.tar.gz
  • cd epicenterDIR
  • if needed, run ./install.sh to copy main executable binary files into "/home/<username>/bin"

Windows

EpiCenter's packages are in ZIP packages. Installation is simply to extract the package to a desired installation location. After extraction, open the extracted folder "epicenterDIR". Then double click the window batch file "launch_epicenter.bat" to launch Windows' Command Line Terminal, where you can run EpiCenter programs.

All programs and documents will be in the folder install_dir/epicenterDIR.


Usage and Documents

  • Usage (type 0-3, 31, 32) for Genome-wide comparison analysis of two samples
    • ./EpiCenter -t analysis_type [options] -i aln_type aln_sample1 aln_sample2
  • Usage (type 4) for read coverage analysis of a single sample
    • ./EpiCenter -t 4 [options] -i aln_type aln_sample
  • Usage (type 5) for converting ChIP/mRNA-seq data files into a data matrix
    • ./EpiCenter -t 5 -f genomic_LOC_info_file [options] -i aln_type aln_file1 [aln_file2 ...]

For details of usages, please refer to EpiCenter user manual(816KB) .


Contact

Leping Li, Ph.D.
Acting Deputy Branch Chief, Biostatistics & Computational Biology Branch and Principal Investigator
Tel 919-541-5168
Fax 919-541-4311
li3@niehs.nih.gov
David M. Umbach, Ph.D.
Staff Scientist
Tel 919-541-4939
umbach@niehs.nih.gov