Question about datasets with multiple single cell RNAseq types (SC3PV2 and SC3PV3)

Question

[hgalmoore]

Hi,

I'm looking at a dataset that has two types of single-cell technology types. Roughly half the samples were run in SC3PV3 and half in SC3PV2. There seems to be a noticeable difference in UMAP in some populations that should be the same. My question is, is it okay to integrate on the 'single-cell type' parameter? I cant really find any info online on how V2 and V3 differ from each other.

[rpolicastro]

scRNA-seq integration methods (e.g. Seurat integration, scVI, fastMNN, etc.) can integrate datasets from different sequencing technologies.