For DNase-seq and ATAC-seq experiments TF footprints can be analyzed with CENTIPEDE [151]. CENTIPEDE is an integrative algorithm for rapid profiling of many TFs simultaneously that combines known information on TF motifs and positional weight matrices, with DNase-seq or ATAC-seq cutting patterns in one unsupervised Bayesian mixture model. Combination of all this information with publicly available expression, DNA methylation and histone modification data can be instrumental for answering questions on epigenetic regulation and inheritance and unveiling long-range patterns of gene regulation and disease development [17, 19, 137]. Finally, multistep sequential data analysis can be generated and stored using Galaxy [164] or Cistrome [165].
