Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes

PLoS Comput Biol. 2019 Feb 19;15(2):e1006731. doi: 10.1371/journal.pcbi.1006731. eCollection 2019 Feb.

Abstract

Graph-based representations are considered to be the future for reference genomes, as they allow integrated representation of the steadily increasing data on individual variation. Currently available tools allow de novo assembly of graph-based reference genomes, alignment of new read sets to the graph representation as well as certain analyses like variant calling and haplotyping. We here present a first method for calling ChIP-Seq peaks on read data aligned to a graph-based reference genome. The method is a graph generalization of the peak caller MACS2, and is implemented in an open source tool, Graph Peak Caller. By using the existing tool vg to build a pan-genome of Arabidopsis thaliana, we validate our approach by showing that Graph Peak Caller with a pan-genome reference graph can trace variants within peaks that are not part of the linear reference genome, and find peaks that in general are more motif-enriched than those found by MACS2.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Arabidopsis / genetics
  • Chromatin Immunoprecipitation / methods*
  • Genome / genetics
  • Genomics / methods*
  • Protein Binding
  • Sequence Analysis, DNA / methods*
  • Software
  • Transcription Factors

Substances

  • Transcription Factors

Grants and funding

This work was supported by the Centre for Computational Inference in Evolutionary Life Science (CELS), but otherwise received no specific grant from any funding agency in the public, commercial, or not-for-profit sectors. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.