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Bioinformatics with R Cookbook by Paurush Praveen Sinha

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Analyzing ChipSeq data

Chromatin immuneprecipitation sequencing (ChipSeq) is a powerful method to identify genome-wide DNA binding sites for a protein of interest. It is often used to determine the binding sites for transcription factors, DNA-binding enzymes, histones, chaperones, or nucleosomes. The workflow to produce the ChipSeq data starts from the cross-links bound proteins and chromatin. The chromatin is fragmented, and the DNA fragments bound to one protein are captured using an antibody specific to it. The ends of the captured fragments are sequenced using NGS. The computational mapping of the sequenced DNA leads to the identification of the genomic locations of these fragments, illuminating their role in DNA protein interactions and epigenetics ...

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