Analyzing ChIP-seq data: Preprocessing, normalization, differential identification, and binding pattern characterization

Cenny Taslim, Kun Huang, Tim Huang, Shili Lin

Research output: Chapter in Book/Report/Conference proceedingChapter

11 Scopus citations


Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a high-throughput antibody-based method to study genome-wide protein-DNA binding interactions. ChIP-seq technology allows scientist to obtain more accurate data providing genome-wide coverage with less starting material and in shorter time compared to older ChIP-chip experiments. Herein we describe a step-by-step guideline in analyzing ChIP-seq data including data preprocessing, nonlinear normalization to enable comparison between different samples and experiments, statistical-based method to identify differential binding sites using mixture modeling and local false discovery rates (fdrs), and binding pattern characterization. In addition, we provide a sample analysis of ChIP-seq data using the steps provided in the guideline.

Original languageEnglish (US)
Title of host publicationNext Generation Microarray Bioinformatics
Subtitle of host publicationMethods and Protocols
EditorsJunbai Wang, Tianhai Tian, Aik Choon Tan
Number of pages17
StatePublished - 2012
Externally publishedYes

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745


  • ChIP-seq
  • Differential analysis
  • Finite mixture model
  • Model-based classification
  • Nonlinear normalization

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology


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