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

Publication Type:

Journal Article

Source:

Bioinformatics (Oxford, England), Volume 29, Issue 16, p.2049-50 (2013)

Keywords:

2013, July 2013, Public Health Sciences Division, Vaccine and Infectious Disease Division

Abstract:

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.