Analysing CITE-seq data where only 4 samples are CITE-seq and rest 11 are scRNA-seq

Question

[Sagrika]

My dataset has total 15 samples but only 4 of them are CITE-seq and rest 11 samples are scRNA-seq. The dataset is from one experiment. I was wondering if someone can suggest how to process the RNA+ADT with integration. My question is

Should I integrate the 4 CITE-seq samples with rest of the samples and perform WNN analysis or separately process the 4 samples?

My downstream goal is annotation, differential analysis and cell-cell interaction for now

I have checked similar github issues issue6832 but that doesn't clarify my question

Any help would be appreciated

Thanks.

Answer 1

[ATpoint]

I would integrate all samples based on the gene expression assay and then visualize the surface protein expression in the clusters, assuming that the four CITE-seq samples are representative for the rest.

I am not aware of actually interating RNA and protein quantitatively. Not saying it does not exist, I just do not know of it, happy to learn otherwise.

[Sagrika]

Thank you for your reply. I will try