Seurat CCA vs rlsi prior to ATAC integration

[LacquerHed]

I was wondering whether using the rlsi reduction during Seurat scRNA-seq integration is most appropriate when considering downstream integration with scATAC-seq in ArchR? Or is CCA also ok? Thanks.

[rcorces]

I dont believe that any of that has an effect on integration. Integration is based on the counts in the RNA matrix, not on the dim red. of the RNA.