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

doi:10.1186/s13059-022-02707-w

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 journal › Article › peer-review

6 Scopus citations

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 language	English (US)
Article number	144
Journal	Genome biology
Volume	23
Issue number	1
DOIs	https://doi.org/10.1186/s13059-022-02707-w
State	Published - 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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10.1186/s13059-022-02707-w

Cite this

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title = "GoPeaks: histone modification peak calling for CUT&Tag",

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.",

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doi = "10.1186/s13059-022-02707-w",

language = "English (US)",

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AU - Yashar, William M.

AU - Kong, Garth

AU - VanCampen, Jake

AU - Curtiss, Brittany M.

AU - Coleman, Daniel J.

AU - Carbone, Lucia

AU - Yardimci, Galip Gürkan

AU - Maxson, Julia E.

AU - Braun, Theodore P.

PY - 2022/12

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AB - 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.

KW - ATAC-seq

KW - CUT&RUN

KW - CUT&Tag

KW - ChIP-seq

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KW - Peak calling

KW - SEACR

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GoPeaks: histone modification peak calling for CUT&Tag

Abstract

Keywords

ASJC Scopus subject areas

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