DANPOS2 with ATAC Seq data?

Question

[Sciurus]

Hi smart folks out there :-)

I was wondering about the analysis of ATAC Seq data and specifically about the step using DANPOS2. It has been developed to analyse MNAse Seq data, right?

But contrary to MNase Seq ATAC Seq data gives me reads where there are NO nucleosomes. Wouldn't this mean that I need to somehow inverse my data to be able to analyze them with DANPOS?

And also for binning the peaks regarding length - wouldn't it only make sense if I binned the area that is NOT covered by reads?

Any help, tips, experience would be great and much appreciated!

Thanks!