This chapter provides an overview the ENCODE project which aims to annotate the entire human genome. It collects DNA sequences using various experimental techniques such as CHIP-seq, RNA-seq, and CAGE-seq. After the data has been obtained it needs to be processed before attempting analysis. The data goes through a number of steps; quality control, peak calling, IDR processing, and blacklist filtering. Once the accuracy of the data has been ensured other analysis can be done in the form of motif discovery, co-association analysis, and signal aggregation over elements.