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This article is part of a special issue on epigenomics.

Open Access Highly Accessed Software

CHANCE: comprehensive software for quality control and validation of ChIP-seq data

Aaron Diaz12, Abhinav Nellore12 and Jun S Song1234*

Author affiliations

1 Institute for Human Genetics, UCSF, 513 Parnassus Avenue, Box 0794, San Francisco, CA 94143-0794, USA

2 The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, 35 Medical Center Way, San Francisco, CA 94143-0525, USA

3 Department of Epidemiology and Biostatistics, UCSF, 185 Berry Street, Lobby 5, Suite 5700, San Francisco, CA 94107, USA

4 Department of Bioengineering and Therapeutic Sciences, UCSF, 513 Parnassus Avenue, San Francisco, CA 94143-0912, USA

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Citation and License

Genome Biology 2012, 13:R98  doi:10.1186/gb-2012-13-10-r98

Published: 15 October 2012

Abstract

ChIP-seq is a powerful method for obtaining genome-wide maps of protein-DNA interactions and epigenetic modifications. CHANCE (CHip-seq ANalytics and Confidence Estimation) is a standalone package for ChIP-seq quality control and protocol optimization. Our user-friendly graphical software quickly estimates the strength and quality of immunoprecipitations, identifies biases, compares the user's data with ENCODE's large collection of published datasets, performs multi-sample normalization, checks against quantitative PCR-validated control regions, and produces informative graphical reports. CHANCE is available at https://github.com/songlab/chance webcite.