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Genome Biol. 2012 Oct 15;13(10):R98. doi: 10.1186/gb-2012-13-10-r98.

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

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.

PMID:
23068444
[PubMed - in process]
PMCID:
PMC4053734
Free PMC Article

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