Integrating and annotating multiple samples of single cell ATAC data
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.
- 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 ?
- 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.
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