The ChIPbinner workflow requires that aligned reads from ChIP-Seq or CUT&RUN/TAG experiments, typically in BAM format, to be binned in uniform windows and converted to BED (Browser Extensible Data) format (minimum BED3 format with chromosome, start and end information) (red box). Users can normalize the raw binned signal. Pairwise comparisons, such as treated versus control (yellow box), can then be performed using genic/intergenic scatterplots, which annotates each bin as genic or intergenic. For comparing more than two samples, PCA or hierarchical clustering can be used to assess consistency of replicates or effect of treatment/mutation on genome-wide profiles of each sample. Next, users can combine replicates for use in downstream analysis (green boxes). After selecting two samples for pairwise comparison, users can identify and annotate clusters of similarly-behaving bins and visualize them. Finally, users can run differential bin analysis and/or select specific clusters of bins for enrichment and depletion analysis
