integration of several multiome datasets

[mengm5]

Hi, I have 4 10X-multiome (scATAC+scRNA) samples. How can I integrate them?

Workflow 1

1. merge 4 scATACs as vignette: https://stuartlab.org/signac/articles/merging
2. integrate 4 scRNAs as vignette: https://satijalab.org/seurat/articles/integration_introduction
3. joint scATACs and scRNAs as vignette: https://stuartlab.org/signac/articles/pbmc_multiomic or vignette: https://stuartlab.org/signac/articles/integrate_atac

Workflow 2

1. joint scATAC and scRNA of each sample to scMultiome as vignette: https://stuartlab.org/signac/articles/pbmc_multiomic
2. integrate 4 samples' scMultiome as vignette: https://stuartlab.org/signac/articles/integrate_atac

Which one to choose?

Best Meng