Fig. 3.

PCR duplicate removal improves biological reproducibility. Pearson correlation representing reproducibility between replicates and mean AUC representing biological information plotted for each footprinting algorithm with and without PCR duplicate removal. Error bars represent 95% confidence interval. a Across all parameter combinations, Pearson correlation coefficients were plotted with and without PCR duplicate removal for each footprinting algorithm. PCR duplicate removal improves biological reproducibility in both HINT and Wellington driven pipelines. b Across all parameter combinations, mean AUC was plotted with and without PCR duplicate removal for each footprinting algorithm. ChIP-seq recovery does not significantly improve in either algorithm with PCR bias correction. AUC-optimized pipelines for HINT use PCR bias correction, while AUC-optimized pipelines for Wellington do not