GoPeaks: histone modification peak calling for CUT&Tag

Genome Biol. 2022 Jul 4;23(1):144. doi: 10.1186/s13059-022-02707-w.

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.

Keywords: ATAC-seq; CUT&RUN; CUT&Tag; ChIP-seq; Epigenetics; GoPeaks; Histone modifications; MACS2; Peak calling; SEACR.

Publication types

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

MeSH terms

  • Chromatin Immunoprecipitation / methods
  • Genome
  • Histone Code*
  • Protein Processing, Post-Translational*
  • Sequence Analysis, DNA / methods