GoPeaks: Histone Modification Peak Calling for CUT&Tag
Yashar, W. M.; Kong, G.; VanCampen, J.; Smith, B. M.; Coleman, D. J.; Carbone, L.; Yardimci, G. G.; Maxson, J. E.; Braun, T. P.
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Genome-wide mapping of the histone modification landscape is critical to understanding tran-scriptional regulation. Cleavage Under Targets and Tagmentation (CUT&Tag) is a new method for profiling the localization of covalent histone modifications, offering improved sensitivity and decreased cost compared with Chromatin Immunoprecipitation Sequencing (ChIP-seq). Here, we present GoPeaks, a peak calling method specifically designed for histone modification CUT&Tag data. GoPeaks implements a Binomial distribution and stringent read count cut-off to nominate candidate genomic regions. We compared the performance of GoPeaks against commonly used peak calling algorithms to detect H3K4me3, H3K4me1, and H3K27Ac peaks from CUT&Tag data. These histone modifications display a range of peak profiles and are frequently used in epigenetic studies. We found GoPeaks robustly detects genome-wide histone modifications and, notably, identifies H3K27Ac with improved sensitivity compared to other standard peak calling algorithms.
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