I have a dataset of multiple tissue samples with paired snRNA and snATAC coming from each individual tissue. The format is 10x without any Multiome approach. I would like to link peaks to a panel of cell-specific genes using LinkPeaks.
I'm wondering whether FindTransferAnchors would work best if done per snRNA/snATAC pair rather than combining all samples together? I can therefore ensure anchors are formed for cells derived from the same tissue rather than across different tissues.
I would then have several co-embedded snRNA/ATAC objects, one per tissue, which I could then merge and run LinkPeaks(). Presumably I would have to unify the peak annotations across tissues at some point too. Would be using ArchR or Signac (preferably the former for speed).
I am not seeing any examples of this anywhere so looking for some feedback on this approach before I get started (it's a huge dataset)
