Bridge integration: joint embedding for clustering?

[epttli]

Hi,

I am using bridge integration (multiome + scATAC) and had a question about obtaining a joint embedding for clustering.

I followed the standard workflow:

PrepareBridgeReference(...)
FindBridgeTransferAnchors(...)
MapQuery(...)

This works well for label transfer and projection (ref.umap), but it only gives a mapped embedding, not a new integrated space.

Is there a way in Seurat to:

• obtain a joint latent space after bridge integration, and
• cluster all cells together in that space?

Or is bridge intended mainly for mapping/annotation, with clustering expected to be done separately (e.g. ATAC-only integration)?

In my data, the bridge projection reveals meaningful structure that other integrations don’t capture, so I’d ideally like to cluster in a bridge-informed space if possible.

Thanks!