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Bioinformatics. 2013 Aug 15;29(16):2049-50. doi: 10.1093/bioinformatics/btt348. Epub 2013 Jun 20.

PING 2.0: an R/Bioconductor package for nucleosome positioning using next-generation sequencing data.

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  • 1Vaccine and Infectious Diseases and Public Health Sciences Divisions, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA.

Abstract

SUMMARY:

MNase-Seq and ChIP-Seq have evolved as popular techniques to study chromatin and histone modification. Although many tools have been developed to identify enriched regions, software tools for nucleosome positioning are still limited. We introduce a flexible and powerful open-source R package, PING 2.0, for nucleosome positioning using MNase-Seq data or MNase- or sonicated- ChIP-Seq data combined with either single-end or paired-end sequencing. PING uses a model-based approach, which enables nucleosome predictions even in the presence of low read counts. We illustrate PING using two paired-end datasets from Saccharomyces cerevisiae and compare its performance with nucleR and ChIPseqR.

AVAILABILITY:

PING 2.0 is available from the Bioconductor website at http://bioconductor.org. It can run on Linux, Mac and Windows.

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