DiffChIPL: a differential peak analysis method for high-throughput sequencing data with biological replicates based on limma.

ABSTRACT:

Motivation

ChIP-seq detects protein-DNA interactions within chromatin, such as that of chromatin structural components and transcription machinery. ChIP-seq profiles are often noisy and variable across replicates, posing a challenge to the development of effective algorithms to accurately detect differential peaks. Methods have recently been designed for this purpose but sometimes yield conflicting results that are inconsistent with the underlying biology. Most existing algorithms perform well on limited datasets. To improve differential analysis of ChIP-seq, we present a novel Differential analysis method for ChIP-seq based on Limma (DiffChIPL).

Results

DiffChIPL is adaptive to asymmetrical or symmetrical data and can accurately report global differences. We used simulated

SUBMITTER: Chen Y 

PROVIDER: S-EPMC9438959 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature