DNase-sequencing is a high-throughput method that allows the genome-wide mapping of open active chromatin by using a DNase-I digestion and the in vivo identification of proteins DNA binding sites that have been protected from enzymatic digestion. This phenomena is called "footprinting". The goal of this master project is the set up of a pipeline for an automated DNase-sequence data analysis, starting with public human stem cells DNase-sequencing data from ENCODE (n=8). Our approach is based on two well known methods: a peak calling program to narrow down the data on the most relevant signal regions, followed by a footprints identification by using a 3-states Hidden Markov Model algorithm. Our preliminary pipeline, though being far from completion, shows already some promising results.