Integrate two dataset with different Number of cells

[yamihn]

Hi everyone,

I have two scRNA‑seq datasets from different batches:

Dataset A: ~8,000 cells

Dataset B: ~60,000 cells

I want to integrate them to perform joint clustering and visualization.

Because the datasets differ so much in size, I’m unsure which strategy is most appropriate to:

Avoid the smaller dataset being dominated by the larger one

Correct batch effects effectively

Preserve biological signals

Could you please advise on the best method or workflow in Seurat 5 for this type of scenario?

Thank you very much for any guidance or examples