Chromatin immunoprecipitation coupled with sequencing (ChIP-seq) is a genomics and epigenomics method to study DNA-protein interactions. ChIP-sequencing uses antibodies that are specific to a protein of interest combined with high-throughput sequencing to map every protein-binding site on a given genome. This method is widely used for the discovery of new regulatory elements such as transcription factors and histone modifications. ChIP-seq data analysis software are essential for data pre-processing and processing (quality control, read alignment, etc.), data analysis, annotation, data visualization and network analysis.
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