Reference mapping

[LucaTucciarone]

I have 10x multimome and 10xsciATACseq. I would like to reference map using Seurat V5, is there a vignette to use bpcells instead of Signac to do so?

[bnprks]

I'm not aware of a vignette to do this, and it sounds like the kind of thing more appropriate to live in the Seurat documentation than the BPCells documentation if you're trying to do reference mapping specifically using Seurat v5.

That being said, there's a lot of overlap in the functionality that can be accomplished with Signac or BPCells, such as import from 10x-format fragment files and creation of peak / tile matrices. My guess would be that if you create a BPCells-backed Seurat object then there's a good chance a lot of the Seurat reference mapping functionality will work. So the main thing you'd need to worry about is making a BPCells equivalent of whatever Signac object is set up during the vignette you have in mind (likely just calculating a peak or tile matrix then making a Seurat object).

For better understanding the BPCells functionality, I'd recommend checking out the intro multiome analysis tutorial or the function documentation. If there's some specific task that the vignette you're following does in Signac that you can't figure out how to replicate in BPCells that's something I'd be better positioned to answer.