To evaluate the overall quality of samples, the peaks of open chromatin regions (OCRs) were called using MACS (v1.4.2)49. For the purpose of quality control analysis, the consensus peakset was created from the individual peaks that were subsequently merged across all samples, retaining only peaks found in at least 2 samples. Subsequently, we counted how many reads for each sample overlapped each consensus peak using featureCounts27 in the Rsubread package50. Finally, we counted fragments defined from paired-end reads that overlapped with the final consensus set of peaks.
