10X multiome subsetting cancer cell line with blacklist_ratio ~ 1 for both hg38_blacklist and hg38_blacklist_unified

[methornton]

Hello! I am processing some cancer cell line 10X plus Mulitome data and I have kind of an outlier as far as the hg38_blacklist_ratio. First, I had to add the metadata from cellranger file 'per_barcode_metrics.csv' file. I used some info from this Q&A site for generating the blacklist_ratio.

# add blacklist ratio and fraction of reads in peaks
ap1$pct_reads_in_peaks <- ap1$atac_peak_region_fragments / ap1$atac_fragments * 100
ap1$blacklist_region_fragments <- FractionCountsInRegion(object = ap1, assay = 'ATAC', regions = blacklist_hg38)
ap1$blacklist_ratio <- ap1$blacklist_region_fragments / ap1$atac_peak_region_fragments

I was able to generate the other QC metrics and here are the images.

Any information or advice is greatly appreciated. The nucleosome values are also fairly low. What does that really mean? To me all of the other values look decent. Did I mess up the blacklist ratio calculation?

TIA