Figure 3

Estimates of covariate effects differ among DNA-seq data types. (a, b) Estimates for the set of BIC selected covariates for the background components of the (a) RNA Pol II ChIP-seq and (b) FAIRE-seq data from chromosome 22 in K562 cells. The set of covariates was standardized to a mean of 0 and variance of 1, which included G/C content ('GC'), mappability score ('Map'), the local background estimate ('BG'), and input control ('Input'). The G/C content covariate (yellow bars) had an opposing effect on the background component for the RNA Pol II (positive) (a) and FAIRE (negative) (b) data. (c, d) Density plots of G/C content (x-axis) versus the natural log of window read count (y-axis) in non-enriched windows (enrichment posterior probability < 0.50) from the (c) RNA Pol II and (d) FAIRE data. Median regression lines fit to the set of background windows from each dataset parallel the ZINBA-estimated relationships between G/C content and signal in background regions.