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Sierra platinum: a fast and robust peak-caller for replicated ChIP-seq experiments with visual quality-control and -steering

Background: Histone modifications play an important role in gene regulation. Their genomic locations are of great interest. Usually, the location is measured by ChIP-seq and analyzed with a peak-caller. Replicated ChIP-seq experiments become more and more available. However, their analysis is based on single-experiment peak-calling or on tools like PePr which allows peak-calling of replicates but whose underlying model might not be suitable for the conditions under which the experiments are performed. Results: We propose a new peak-caller called \"Sierra Platinum\" that allows peak-calling of replicated ChIP-seq
experiments. Moreover, it provides a variety of quality measures together with integrated visualizations supporting the assessment of the replicates and the resulting peaks, as well as steering the peak-calling process. Conclusion: We show that Sierra Platinum outperforms currently available methods using a newly generated benchmark data set and using real data from the NIH Roadmap Epigenomics Project. It is robust against noisy replicates.

Identiferoai:union.ndltd.org:DRESDEN/oai:qucosa:de:qucosa:15195
Date January 2016
CreatorsMüller, Lydia, Gerighausen, Daniel, Farman, Mariam, Zeckzer, Dirk
ContributorsUniversität Leipzig
PublisherBioMed Central
Source SetsHochschulschriftenserver (HSSS) der SLUB Dresden
LanguageEnglish
Detected LanguageEnglish
Typedoc-type:article, info:eu-repo/semantics/article, doc-type:Text
SourceBMC Bioinformatics (2016) 17:377 DOI 10.1186/s12859-016-1248-6
Rightsinfo:eu-repo/semantics/openAccess

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