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

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)

• 64-bit system
  • Linux packages: epicenter_Linux64.tar.gz(4MB)
  • MacOS X packages: epicenter_MacOS64.tar.gz(3MB)
  • Windows packages: epicenter_Win64.zip(6MB)
• 32-bit system
  • Linux packages: epicenter_Linux32.tar.gz(4MB)
  • MacOS X packages: epicenter_MacOS32.tar.gz(3MB)
  • Windows packages: epicenter_MacOS64.tar.gz(3MB)

Version 1-6-1-8

• 64-bit system
  • Linux packages: epicenter_Linux64.tar.gz(4MB)
  • MacOS X packages: epicenter_MacOS64.tar.gz(3MB)
  • Windows packages: epicenter_Win64.zip(6MB)
• 32-bit system
  • Linux packages: epicenter_Linux32.tar.gz(4MB)
  • MacOS X packages: epicenter_MacOS32.tar.gz(3MB)
  • Windows packages: epicenter_Win32.zip(3MB)

Version 1-5-9-8

• 64-bit system
  • Linux packages: epicenter_Linux64.tar.gz(2MB)
  • MacOS X packages: epicenter_MacOS64.tar.gz(1MB)
  • Windows packages: epicenter_Win64.zip(4MB)
• 32-bit system
  • Linux packages: epicenter_Linux32.tar.gz(2MB)
  • MacOS X packages: epicenter_MacOS32.tar.gz(1MB)
  • Windows packages: epicenter_Win32.zip(1MB)

Version 1-5-8-8

• 64-bit system
  • Linux packages: epicenter_Linux64.tar.gz(2MB)
  • MacOS X packages: epicenter_MacOS64.tar.gz(1MB)
  • Windows packages: epicenter_Win64.zip(4MB)
• 32-bit system
  • Linux packages: epicenter_Linux32.tar.gz(2MB)
  • MacOS X packages: epicenter_MacOS32.tar.gz(1MB)
  • Windows packages: epicenter_Win32.zip(1MB)

Version 1-5-7-8

• 64-bit system
  • Linux packages: epicenter_Linux64.tar.gz(2MB)
  • MacOS X packages: epicenter_MacOS64.tar.gz(1MB)
  • Windows packages: epicenter_Win64.zip(4MB)
• 32-bit system
  • Linux packages: epicenter_Linux32.tar.gz(2MB)
  • MacOS X packages: epicenter_MacOS32.tar.gz(1MB)
  • Windows packages: epicenter_Win32.zip(1MB)

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

Weichun Huang, Ph.D.
Staff Scientist

Tel (919) 541-4943
huang6@niehs.nih.gov

Leping Li, Ph.D.
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