Chunk #61 — Online Methods — 1. Data matrix, primary analysis and processing, quality control — 1.2 ChIP-seq and DNase-seq uniform reprocessing for consolidated epigenomes — e. Quality Control
To identify potential antibody cross-reactivity or mislabeling issues, a pairwise correlation heatmap (Extended Data 1e) was computed across all consolidated datasets for H3K4me1, H3K4me3, H3K36me3, H3K27me3, H3K9me3, H3K27ac, H3K9ac, and DNase. We computed the Pearson correlation between all pairs of the signal tracks based on signal in chr 1-22 and chrX. We used the signal confidence score tracks (-log10(Poisson p-value)) where we first computed the average signal scores within each consecutive 25-bp interval. To order the experiments in the heatmap we defined the distance between two pairs of experiments as 1-correlation value and used a traveling salesman problem formulation104.
