Bioinformatics Core Workflow for ChIP-Seq Data Analysis
1Institute of Epigenetics and Stem Cells, Helmholtz Munich, Munich, Germany. tamas.schauer@helmholtz-munich.de.
Methods in Molecular Biology (Clifton, N.J.)
|August 14, 2024
Abstract:
Chromatin immunoprecipitation (ChIP) followed by next-generation sequencing (-seq) has been the most common genomics method for studying DNA-protein interactions in the last decade. ChIP-seq technology became standard both experimentally and computationally. This chapter presents a core workflow that covers data processing and initial analytical steps of ChIP-seq data. We provide a step-by-step protocol of the commands as well as a fully assembled Snakemake workflow. Along the protocol, we discuss key tool parameters, quality control, output reports, and preliminary results.
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