@article{b8b1ba344fcd480e914add346c9d582e,
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.",
keywords = "ATAC-seq, CUT&RUN, CUT&Tag, ChIP-seq, Epigenetics, GoPeaks, Histone modifications, MACS2, Peak calling, SEACR",
author = "Yashar, {William M.} and Garth Kong and Jake VanCampen and Curtiss, {Brittany M.} and Coleman, {Daniel J.} and Lucia Carbone and Yardimci, {Galip G{\"u}rkan} and Maxson, {Julia E.} and Braun, {Theodore P.}",
note = "Funding Information: Funding was provided by an American Society of Hematology Research Restart Award, an American Society of Hematology Scholar Award and 1 K08 CA245224 from NCI awarded to TPB. WMY was supported by NIH T32 GM109835: Medical Scientist Training Program of Oregon Health and Science University. Funding Information: We thank the following OHSU core facilities for their assistance: Massive Parallel Sequencing Shared Resource, ExaCloud Cluster Computational Resource, and the Advanced Computing Center. Andrew Cosgrove was the primary editor of this article and managed its editorial process and peer review in collaboration with the rest of the editorial team. The review history is available as Additional file 3. Publisher Copyright: {\textcopyright} 2022, The Author(s).",
year = "2022",
month = dec,
doi = "10.1186/s13059-022-02707-w",
language = "English (US)",
volume = "23",
journal = "Genome Biology",
issn = "1474-7596",
publisher = "BioMed Central",
number = "1",
}