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Rapid innovation in ChIP-seq peak-calling algorithms is outdistancing benchmarking efforts

Szalkowski, A. M. and Schmid, C. D.. (2011) Rapid innovation in ChIP-seq peak-calling algorithms is outdistancing benchmarking efforts. Briefings in bioinformatics, Vol. 12, H. 6. pp. 626-633.

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Official URL: http://edoc.unibas.ch/dok/A6002318

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Abstract

The current understanding of the regulation of transcription does not keep the pace with the spectacular advances in the determination of genomic sequences. Chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-seq) promises to give better insight into transcription regulation by locating sites of protein-DNA interactions. Such loci of putative interactions can be inferred from the genome-wide distributions of ChIP-seq data by peak-calling software. The analysis of ChIP-seq data critically depends on this step and a multitude of these peak-callers have been deployed in the recent years. A recent study reported severe variation among peak-calling results. Yet, peak-calling still lacks systematic quantitative benchmarking. Here, we summarize benchmarking efforts and explain potential drawbacks of each benchmarking method
Faculties and Departments:09 Associated Institutions > Swiss Tropical and Public Health Institute (Swiss TPH) > Department of Epidemiology and Public Health (EPH) > Infectious Disease Modelling > Infectious Disease Modelling (Smith)
UniBasel Contributors:Schmid, Christoph
Item Type:Article, refereed
Article Subtype:Research Article
Bibsysno:Link to catalogue
Publisher:Oxford University Press
ISSN:1467-5463
Note:Publication type according to Uni Basel Research Database: Journal article
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Last Modified:08 Nov 2012 16:23
Deposited On:08 Nov 2012 16:17

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