Fig. 6.

Impact of ChIP-seq recovery optimization on ATAC-seq and DNase1-seq footprinting performance. a Per-TF ChIP-seq recovery for ATAC-seq pipelines. b Per-TF ChIP-seq recovery for DNase1-seq pipelines. c ROC curves for ATAC-seq ChIP recovery. d ROC curves for DNase1-seq ChIP recovery. There is an imbalance between negative TFBSs and positive TFBSs of approximately 10:1, and footprint algorithms are conservative and tend towards specificity over sensitivity