Figure 3
Comparison of different iterations of the ATAC-seq protocol with DNase-seq. (a) Overlap of chicken lung peaks called from 30 million reads derived from DNase-seq and ATAC-seq protocols 1 and 3 (libraries 1-a-50K and 3-e-200K) (minimum 1 bp overlap). (b) Fraction of reads in peaks (FRiP) that overlap (minimum 1 bp) promoters (±2 kb from TSS) and distal elements (>2 kb from TSS) from libraries generated using different iterations of ATAC-seq; ***P < 0.001 by two-tailed unpaired Student’s t-test comparing the fraction of reads in peaks to reads outside of peaks. All values were determined from 40 million random aligned de-duplicated reads. (c) ATAC-seq quality metrics: estimated library size (“Lib size”; purple), percentage of reads that mapped to mitochondrial DNA (“% Mito”; blue), enrichment of signal at promoters (2 kb upstream from TSS; orange; Ensembl Galgal5.0.94 annotation; minimum 1 bp overlap of ATAC-seq peak with promoter), and FRiP (green). Desirable values are shaded darker, with the scale starting at 0 (white) and ending at the maximum value. For the percent mitochondrial reads, anything below 5% is shaded blue. All values were determined from 5 million random aligned reads.
