something about integrating scATAC-seq into scRNA-seq

[tianchen2019]

I would like to ask why when integrating scATAC-seq into scRNA-seq data, a large number of cells(scATAC-seq) are integrated into the same cell (scRNA-seq).
i have a scATAC-seq of 380000 cells, and only integrated 23000 scRNA-seq cells.

[rcorces]

Integration in ArchR is managed through Seurat's infrastructure (FindTransferAnchors()). The best matching cell from RNA-space is used for each cell in ATAC-space. Presumably there is a small subset of cells in your RNA-space that are repeatedly serving as the best match for your ATAC cells. This could be data quality or it could be that you need to tweak parameters in addGeneIntegrationMatrix().
https://www.archrproject.com/reference/addGeneIntegrationMatrix.html