A computational pipeline to visualize DNA-protein binding states using dSMF data

Here, we present a pipeline to map states of protein-binding DNA in vivo. Our pipeline infers as well as quantifies cooperative binding. Using dual-enzyme single-molecule footprinting (dSMF) data, we show how our workflow identifies binding states at an enhancer in Drosophila S2 cells. Data from cells lacking endogenous DNA methylation are a prerequisite for this pipeline. For complete details on the use and execution of this protocol, please refer to Rao et al. (2021) and Krebs et al. (2017).