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

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

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • High-Throughput Nucleotide Sequencing / methods*
  • Nucleosomes / chemistry*
  • Saccharomyces cerevisiae / genetics
  • Sequence Analysis, DNA / methods*
  • Software*

Substances

  • Nucleosomes