Figure 2: Quality control, enrichment analysis, and reproducibility for ChIP-seq and ChIP-exo data.
From: ChIP-seq and ChIP-exo profiling of Pol II, H2A.Z, and H3K4me3 in human K562 cells
(a) Box-plot distribution of base quality scores are shown for Pol II ChIP-exo replicate 1. A score greater than 30 (green region) indicates a high confidence base call. (b) ChIP-enrichment analysis plot that displays the cumulative percent of total reads found in a given percent of the mappable human genome. No ChIP enrichment would result in a diagonal trace. (c) Scatter plot correlation analysis for Pol II ChIP-exo biological replicates as measured by the Spearman correlation coefficient R-values (upper right corner).
