Fig. 4

Impact of HOMER peak parameters on reproducibility. Assessment of the impact of HOMER peak sizes on DNase1-seq and ATAC-seq isogenic reproducibility. a Pearson correlation coefficients for average peak height in genomic bins was measured for each peak size parameter for all parameter combinations, for each data type. b Distributions of Pearson correlation coefficients between replicates are plotted for each peak size. Smaller peak sizes result in higher reproducibility of the openness of 10 kb genomic windows between replicates. Results are shown in one plot for both DNase1-seq and ATAC-seq. Note that ATAC-seq replicates were produced within one lab whereas the DNase1-seq libraries were from two ENCODE groups