How to analyze 3_Controls and 3_treatment multiome how to analyze togethet?

[zara03]

I am analyzing a 10X single cell multiome datasets carried out in 3ctrl and 3 treated cell linds, after running standard cellranger pipeline for generating counts file and atac fragments.

I am wondering how to analyze them together or i have to analyze one by one like ctrl_1 , then ctrl_2 and then ctrl_3. same for treated.
Because I want to link peaks to genes and i want to show two heat maps, one as average of Ctrl and one as average of treated.

Please guide.