I'm wondering about the "single-end" single cell ATAC-seq (scATAC-seq) analysis. The reads obtained from each cell is at most 1 read at each region, by nature.
Some paired-end scATAC-seq pipelines execute the peak-calling by MACS2 etc., but it seems to be hard to detect peaks from single-end single cell data. Actually, the sum of obtained peak region was about only 3% of the read coverage simply calculated by bedtools bamtobed when I tried with my sample data.
Then, how should I treat the "open chromatin region" of each single cell?
Calculate the peak region with the aggregate of single cell, and then consider whether there is a read in each cell by bedtools intersect is the best?