Fig. 2

Strategies for cleavage bias correction. Comparison of bias estimation methods in standard ATAC-seq (a) and DNase-seq (b) on 32 TF ChIP-seq data sets from GM12878 cells. The y-axis denotes the ranking score, where higher values indicate higher recovery of footprints supported by TF ChIP-seq peaks. Numbers after methods names (x-axis) indicate optimal word size (k). p values are based on the Friedman-Nemenyi test (see Additional file 1: Table S1–S12 for complete results). c The scatter plot contrasting AUPR of HINT with PDM-based estimation with 8-mers (y-axis) and HINT without bias correction (x-axis) in GM12878 cells. d Bias estimates and average ATAC-seq signals centered around NFYB and SP1 motifs supported by a ChIP-seq peaks in GM12878 cells. e Precision-recall curve also supports the improvement in prediction of SP1 ChIP-Seq supported binding sites with cleavage bias correction. f ATAC-seq cleavage signals and footprint predictions with (HINT-PDM) and without (HINT) bias correction in two selected genomic regions. Footprint predictions on bias-corrected signals match SP1 motifs supported by ChIP-seq peaks, while no footprints are predicted in uncorrected ATAC-seq due to the presence of cleavage sites within the SP1 motif