GoPeaks: histone modification peak calling for CUT&Tag

William M. Yashar, Garth Kong, Jake VanCampen, Brittany M. Curtiss, Daniel J. Coleman, Lucia Carbone, Galip Gürkan Yardimci, Julia E. Maxson, Theodore P. Braun

Research output: Contribution to journalArticlepeer-review

Abstract

Genome-wide mapping of histone modifications is critical to understanding transcriptional regulation. CUT&Tag is a new method for profiling histone modifications, offering improved sensitivity and decreased cost compared with ChIP-seq. Here, we present GoPeaks, a peak calling method specifically designed for histone modification CUT&Tag data. We compare the performance of GoPeaks against commonly used peak calling algorithms to detect histone modifications that display a range of peak profiles and are frequently used in epigenetic studies. We find that GoPeaks robustly detects genome-wide histone modifications and, notably, identifies a substantial number of H3K27ac peaks with improved sensitivity compared to other standard algorithms.

Original languageEnglish (US)
Article number144
JournalGenome biology
Volume23
Issue number1
DOIs
StatePublished - Dec 2022

Keywords

  • ATAC-seq
  • CUT&RUN
  • CUT&Tag
  • ChIP-seq
  • Epigenetics
  • GoPeaks
  • Histone modifications
  • MACS2
  • Peak calling
  • SEACR

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

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