Paired-end data for peak calling

[09oulin]

Hello,

This is really an excellent work. And thanks for making detailed code public.

I have a question about peak calling in data preprocessing "snakemake file". I am confused why you use "BAMPE" and "BED" in macs2. Besides, if I want to call peaks for my scATAC-seq paired-end data using bed files but not using bam files (because they are really too big), how should I do in this step? Use the "BED" or "BEDPE" to format argument？Could you please give me some advice?

Thank you for time!

Lin Ou