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Bioinformatics Advance Access originally published online on July 3, 2008
Bioinformatics 2008 24(15):1729-1730; doi:10.1093/bioinformatics/btn305
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology

Anthony P. Fejes 1,*, Gordon Robertson 1, Mikhail Bilenky 1, Richard Varhol 1, Matthew Bainbridge 2 and Steven J. M. Jones 1,*

1Genome Sciences Centre, BC Cancer Agency, Suite 100 570 West 7th Avenue, Vancouver, British Columbia, Canada V5Z 4S6 and 2College of Medicine, Houston, Texas, One Baylor Plaza, MS: BCM215, Houston, TX 77030, USA

*To whom correspondence should be addressed.


  Abstract

Summary: Next-generation sequencing can provide insight into protein–DNA association events on a genome-wide scale, and is being applied in an increasing number of applications in genomics and meta-genomics research. However, few software applications are available for interpreting these experiments. We present here an efficient application for use with chromatin-immunoprecipitation (ChIP-Seq) experimental data that includes novel functionality for identifying areas of gene enrichment and transcription factor binding site locations, as well as for estimating DNA fragment size distributions in enriched areas. The FindPeaks application can generate UCSC compatible custom ‘WIG’ track files from aligned-read files for short-read sequencing technology. The software application can be executed on any platform capable of running a Java Runtime Environment. Memory requirements are proportional to the number of sequencing reads analyzed; typically 4 GB permits processing of up to 40 million reads.

Availability: The FindPeaks 3.1 package and manual, containing algorithm descriptions, usage instructions and examples, are available at http://www.bcgsc.ca/platform/bioinfo/software/findpeaks Source files for FindPeaks 3.1 are available for academic use.

Contact: afejes{at}bcgsc.ca

Associate Editor: Alfonso Valencia

Received on March 19, 2008; revised on May 8, 2008; accepted on June 9, 2008

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