PWMs combined with all ENCODE DNase-seq data sets were run through CENTIPEDE to generate footprint calls (Pique-Regi et al. 2011). In addition to the DNase-seq data, the PWM score and conservation score (average phastCons score across the aligned bases) were provided to CENTIPEDE. Only those footprints with a posterior probability ≥ 0.99 were retained.
