GoPeaks: histone modification peak calling for CUT&Tag

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...

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Detalles Bibliográficos
Autores principales: Yashar, William M., Kong, Garth, VanCampen, Jake, Curtiss, Brittany M., Coleman, Daniel J., Carbone, Lucia, Yardimci, Galip Gürkan, Maxson, Julia E., Braun, Theodore P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9252088/
https://www.ncbi.nlm.nih.gov/pubmed/35788238
http://dx.doi.org/10.1186/s13059-022-02707-w
Descripción
Sumario: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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-022-02707-w.

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