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bioRxiv · 10.1101/2022.01.10.475735

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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Abstract

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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Yashar, W. M., Kong, G., VanCampen, J., Smith, B. M., Coleman, D. J., Carbone, L., Yardimci, G. G., Maxson, J. E., Braun, T. P.. 2022-01-12. GoPeaks: Histone Modification Peak Calling for CUT&Tag. https://doi.org/10.1101/2022.01.10.475735

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