DNase-capture reveals differential transcription factor binding modalities
DNase-seq (left), DNase-capture (right), and CTCF ChIP-seq data (center) CTCF motif hits ranked by the number of CTCF ChIP-seq reads in the region. Many DNase-capture profiles are clearer than their DNase-seq counterparts. The bottom half shows CTCF motif matches, but are not called by GEM. The data pre-correction was used here. The legend in the figure shows the motif hit counts scale, with dark red representing more hits, and dark blue representing fewer hits. Note that the footprints represented in lines 4, 34, 44, and 45 are significantly better defined in the DNase-capture data than in the DNase-seq data.