FindPeaks

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

Project Description

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.

Dependencies:

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.

Errata:

• In some cases, the FDR file for version 3.1.9.2 contains an extra column header "Rand", after "Rand.sum", which should be removed.

History:

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 http://vancouvershortr.sourceforge.net/ for current versions, news support.