Skip to main content

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
Back to article page

BMC Bioinformatics

ISSN: 1471-2105

Contact us