Comparing control vs treatment for 10x Multiome (RNA + ATAC) datasets

Question

[mc2548]

I have two multiome datasets (sn RNA and ATAC) - one for my treatment group and the other for my control. I'm interested in GEX analysis that is similar to this (https://satijalab.org/seurat/v3.2/immune_alignment.html). However the tutorial deals with a pre-existing dataset "ifnb". I am trying to figure out how from my cellranger count outputs I can come up with a data format like "ifnb" which somehow form the look of it combines two datasets.

[GenoMax]

Since this is a relatively new kit you may need to follow cellranger arc protocol described here. seurat may not have an equivalent available as yet but someone more familiar with seurat will likely chime in soon.