@inbook{1051923b6ff74c3884753b10c491b77c,
title = "Analyzing ChIP-seq data: Preprocessing, normalization, differential identification, and binding pattern characterization",
abstract = "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.",
keywords = "ChIP-seq, Differential analysis, Finite mixture model, Model-based classification, Nonlinear normalization",
author = "Cenny Taslim and Kun Huang and Tim Huang and Shili Lin",
year = "2012",
doi = "10.1007/978-1-61779-400-1_18",
language = "English (US)",
isbn = "9781617793998",
series = "Methods in Molecular Biology",
pages = "275--291",
editor = "Junbai Wang and Tianhai Tian and Tan, {Aik Choon}",
booktitle = "Next Generation Microarray Bioinformatics",
}