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peaksat: an R package for ChIP-seq peak saturation analysis by Joseph R Boyd; Cong Gao; Kathleen Quinn; Andrew Fritz; Janet Stein; Gary Stein; Karen Glass; Seth Frietze is a Biochemistry, Genetics and Molecular Biology article available to read on EtoBox.

What is peaksat: an R package for ChIP-seq peak saturation analysis about?

## Abstract ## Background Epigenomic profiling assays such as ChIP-seq have been widely used to map the genome-wide enrichment profiles of chromatin-associated proteins and posttranslational histone modifications. Sequencing depth is a key parameter in experimental design and quality control. However, due to variable sequencing depth requirements across experimental conditions, it can be challenging to determine optimal sequencing depth, particularly for projects involving multiple targets or cell types. ## Results We developed the __peaksat__ R package to provide target read depth estimates for epigenomic experiments based on the analysis of peak saturation curves. We applied __peaksat__ to establish the distinctive read depth requirements for ChIP-seq studies of histone modifications in different cell lines. Using __peaksat,__ we were able to estimate the target read depth required per library to obtain high-quality peak calls for downstream analysis. In addition, __peaksat__ was applied to other sequence-enrichment methods including CUT&RUN and ATAC-seq. ## Conclusion __peaksat__ addresses a need for researchers to make informed decisions about whether their sequencing data has

Who reads peaksat: an R package for ChIP-seq peak saturation analysis?

Author

Joseph R Boyd; Cong Gao; Kathleen Quinn; Andrew Fritz; Janet Stein; Gary Stein; Karen Glass; Seth Frietze

Publisher

Springer Science and Business Media LLC

Published

2023

Language

EN

Field

Biochemistry, Genetics and Molecular Biology (Life Sciences)