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  • Title: Analyzing ChIP-seq data: preprocessing, normalization, differential identification, and binding pattern characterization.
    Author: Taslim C, Huang K, Huang T, Lin S.
    Journal: Methods Mol Biol; 2012; 802():275-91. PubMed ID: 22130887.
    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.
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