Integrating and annotating multiple samples of single cell ATAC data

Question

[AB]

Hi,

I have paired single cell RNASeq and single cell ATAC data. They are not multiomic. I'm trying to integrate and annotate my scRNA and scATAC data.

1. Would it be appropriate to perform cross-modality integration and label transfer for each sample and then integrate all the samples or integrate all scATAC, integrate all scRNA and then perform the integration and label transfer ?
2. I tried the former method and that left some of my cells unannotated with NA's. How can i go back in an re-annotate them ? Subset them out and look at markers?

Appreciate any feedback.