Question on multiple data source integration

[levinhein]

Hello. I just want to clarify, because I'm integrating different types of public single cell data. Two sources have the individual data for all their samples available, but one other source only has a single .h5ad file containing all sample data (already merged/integrated). All of these I already converted into Seurat format.

I want to integrated all the 3 sources. The first two sources, no problem because they are individual samples data, but I'm not sure how to process the third.

What is the recommended thing to do here? Should I separate the third source (merged file) into individual samples before doing the full integration of all data?

[NeuralBind]

I have a similar issue, i just started using seurat i try now with merge and then integrate with DataIntegration, while the vignettes in the LayerIntegration are making distinct layers of the RNA assay based on an condition/method column.