SpikChIP: a novel computational methodology to compare multiple ChIP-seq using spike-in chromatin.

ABSTRACT: In order to evaluate cell- and disease-specific changes in the interacting strength of chromatin targets, ChIP-seq signal across multiple conditions must undergo robust normalization. However, this is not possible using the standard ChIP-seq scheme, which lacks a reference for the control of biological and experimental variabilities. While several studies have recently proposed different solutions to circumvent this problem, substantial analytical differences among methodologies could hamper the experimental reproducibility and quantitative accuracy. Here, we propose a computational method to accurately compare ChIP-seq experiments, with exogenous spike-in chromatin, across samples in a genome-wide manner by using a local regression strategy (spikChIP). In contrast to the previous methodol

SUBMITTER: Blanco E 

PROVIDER: S-EPMC8315120 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature