Subclustering ArchR project based on Gene Integration Matrix

[LacquerHed]

I am trying to come up with a good strategy to do this, and I see two potential avenues, just not sure which is more appropriate:

1. Subset my scRNA-seq dataset and ArchrR project by the specific cluster of interest and integrate

2. Subset the total ArchR project for cluster of interest after integration with full scRNA-seq dataset

Thanks for your help.

[rcorces]

I dont think there is a single correct answer for this. Option 1 would be fine if you knew that the subcluster in RNA was exactly the same as the subcluster in ATAC and would be suitable for constrained integration. Otherwise I might opt for Option 2