How to merge two species of scATAC data

Question

[星月]

Hi, I have two species of single-cell ATAC data. I would like to know how can I integrate these two single cell ATAC data across species correctly, when I extract the corresponding gene activity matrix using the basic process of signac, and then integrate it using the integration method of CCA of seurat, although the species will be clustered together, the UMAP graphs will show clawed clusters of anomalies, is it because of the pre-filtering thresholds are not strict enough or is it because the CCA cannot perform this cross-species integration of scATAC data. Or is there another method of integrating scATAC across species that works better.Thanks!

[bk11]

You can check Method Discussed in SATURN. You should definitely try different approaches and select the best one that works for your data.