ChIP-AP: an integrated analysis pipeline for unbiased ChIP-seq analysis.

ABSTRACT: Chromatin immunoprecipitation coupled with sequencing (ChIP-seq) is a technique used to identify protein-DNA interaction sites through antibody pull-down, sequencing and analysis; with enrichment 'peak' calling being the most critical analytical step. Benchmarking studies have consistently shown that peak callers have distinct selectivity and specificity characteristics that are not additive and seldom completely overlap in many scenarios, even after parameter optimization. We therefore developed ChIP-AP, an integrated ChIP-seq analysis pipeline utilizing four independent peak callers, which seamlessly processes raw sequencing files to final result. This approach enables (1) better gauging of peak confidence through detection by multiple algorithms, and (2) more thoroughly surveys the bind

SUBMITTER: Suryatenggara J 

PROVIDER: S-EPMC8769893 | biostudies-literature | 2022 Jan

REPOSITORIES: biostudies-literature