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Table 2 We computed the pairwise covariance between read densities in 250 bp windows and among weights of overlapping open chromatin peaks (using F-seq) before and after bias correction

From: Correcting nucleotide-specific biases in high-throughput sequencing data

  Read density Peak weight
  Raw Corrected Raw Corrected
DNase vs. ChIP 0.2967 0.3112 0.3784 0.4138
DNase vs. FAIRE 0.3157 0.3105 0.6300 0.6029
DNase vs. ATAC 0.5268 0.5387 0.6620 0.6623
ChIP vs. FAIRE 0.1563 0.1589 0.2072 0.2214
ChIP vs. ATAC 0.2137 0.2182 0.2982 0.3138
FAIRE vs. ATAC 0.2700 0.2731 0.4637 0.4757
  1. Correlations are shown between DNase-seq, FAIRE-seq, ATAC-seq, and ChIP-seq for a generic promoter, CTCF. Since these assays all target or are enriched in regions of open chromatin, we see convergence of these signals after correction