Selecting ChIP-seq normalization methods from the perspective of their technical conditions.

ABSTRACT: Chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) provides insights into both the genomic location occupied by the protein of interest and the difference in DNA occupancy between experimental states. Given that ChIP-seq data are collected experimentally, an important step for determining regions with differential DNA occupancy between states is between-sample normalization. While between-sample normalization is crucial for downstream differential binding analysis, the technical conditions underlying between-sample normalization methods have yet to be examined for ChIP-seq. We identify three important technical conditions underlying ChIP-seq between-sample normalization methods: balanced differential DNA occupancy, equal total DNA occupancy, and equal background bindi

SUBMITTER: Colando S 

PROVIDER: S-EPMC12368857 | biostudies-literature | 2025 Jul

REPOSITORIES: biostudies-literature