Custom Reference Genome in ArchR

[mano2991]

I have created a custom reference genome for Cell Ranger ATAC by appending the transgene information to the mouse reference genome (mm10) and modifying the GTF file accordingly. The output from cellranger-atac count includes a BAM file where I can see my transgene and GFP reads. These features are also visible in the feature plot within the Loupe Browser.

However, I am unable to achieve the same results in ArchR. I would appreciate any guidance on creating a custom reference genome in ArchR to visualize these transgene features.

Thank you in advance for your assistance.