Q: How many fragments are generally sufficient for hmmratac function?

[leqi0001]

Hi,

I have a big cohort of scATACseq data, totaling 1 billion fragments from 24 pools of experiments (24 billion total). I've been trying to run hmmratac on these 24 fragment files with --cutoff-analysis-only, but it has been a week. The log says it downsampled to 800 million fragments for training, but the step to generate short, mono-, di-, and tri-nucleosomal signals has run for 3 days. Should I downsample the fragments files before hmmratac? There must be diminishing returns with more fragments, but I'm not sure how to decide the degree of downsampling.

Appreciate any suggestions!