Help. I am still new to the concept of scATAC-seq and was wondering if anyone could provide a straightforward workflow. I am referring to the Signac vignettes but it seems to go back and forth between tutorials.

I am starting out with 2 samples-- one knockout and the other wildtype. I have also called for peaks through MACS2. Where do I go from here up until DARs? Where do I merge? How to integrate scATAC/scRNA data with peaks information.

*Step by step please.