We computed the nucleosome signal score and TSS enrichment score for each cell as described above. We retained cells with a TSS enrichment score > 1, a nucleosome signal score <2, between 5,000 and 70,000 total ATAC-seq counts (based on the 10x Cellranger ATAC-seq count matrix) and between 1,000 and 25,000 total RNA counts.
