Please Note: FindPeaks is now being maintained as part of the open source Vancouver Short Read Analysis Package Project at SourceForge - Please go to for the project's new web page.

FindPeaks performs two functions:

  1. Analysis of short-read sequencing (Solexa/Illumina) experiments to identify areas of enrichment
  2. Generating wig files for use with the UCSC browser.

Findpeaks was developed to perform analysis of ChIP-Seq experiments. It uses a naive algorithm for identifying regions of high coverage, which represent Chromatin Immunoprecipitation enrichment of sequence fragments, indicating the location of a bound protein of interest.  A minimum height threshold is used to determine which "peaks" are shown in the UCSC compatible wig file - if no threshold is use, all reads are shown.  It collects and sorts the reads along each chromosomes, and identifies areas of enrichment, termed "Peaks".  These peaks are particularly important in Chromatin Immunoprecipiation experiments (ChIP-Seq or ChIP-Solexa experiments), as they indicate the location of a bound protein of interest.


Findpeaks uses several utilities to process Eland alignment files. These programs exist as stand alone java files created by Matthew Bainbridge, which result in the creation of "coord" files. In addition, The current version of Findpeaks also depends on several coord processing libraries. These dependencies are expected to be removed in future releases.


  • In some cases, the FDR file for version contains an extra column header "Rand", after "Rand.sum", which should be removed.


Version 1.0 was written by Matthew Bainbridge, and provided "good enough" location finding of peaks.

Version 2.0 is a complete rewrite of the code in Java (written and maintained by Anthony Fejes), following Sun Java coding standards, and has been extensively QA'd for accuracy and completeness. It provides a significant speed improvement, as well as improved documentation and maintainability. There are no outstanding bugs in this release.

Version 3.1.x provides many updates in functionality, including creation of banners, directional peak finding, customized peak trimming and subpeak identification.  

Version 3.2.x is now being developed under the GPL at sourceforge.  Please visit for current versions, news support.

Current Release

Released May 09, 2008

FindPeaks and Supporting Files
For all platforms (165.8 KB)

Replacement for SeparateElandReads to allow use of s_x_sorted.txt files from Eland 0.4+
For all platforms (9.8 KB)

Release Notes

  • Minor release fixing a bug in the FDR calculation, whereby FDR values  were not normalized by the number of iterations run
  • Updated description of FDR in manual
  • Added SeparateElandSortedRead.jar to convert s_x_sorted.txt files to the old eland format while performing the separate chromosome functionality, allowing the sorted flles to be used with the FindPeaks application. This file is for FindPeaks only  - Native support for Eland 0.4+ file formats is integrated in FP3.2

All Releases

Version Released Description Licenses Status May 09, 2008 Bug fix and manual update. BCCA final
3.1.9 May 06, 2008 This is the final release in the 3.1.x line.
Rebuilt core peak locator algorithms for more robust peak locating, and greater speed.
BCCA final
3.1.8 Apr 18, 2008 This is not a final release. Experimental releases should only be used for testing and development. Do not use these on production sites, and make sure you have proper backups before installing. BCCA release-candidate
2.1.3 Dec 05, 2007 Last release in the 2.x line.
Better able to handle FDR calculations for large datasets, fixes incorrect casting.
GPL final
Back to top