scATAC-seq workflow

Question

[bioinformatics.girl]

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.

[Pierre Lindenbaum]

if anyone could provide a straightforward workflow

https://www.frontiersin.org/articles/10.3389/fcell.2022.981859/full "scATACpipe: A nextflow pipeline for comprehensive and reproducible analyses of single cell ATAC-seq data"

[bioinformatics.girl]

I've read this. Clearly I'm looking for a straightforward step-by-step clarification of the processing. Starting from my data that I briefly outlined.