Integrating multimodal data from multiple samples

[bapoorva]

Hi,
I have 10 samples with scRNA and 7 samples with scATAC data. Out of the 10, 2 are multiome, 5 are paired scRNA and scATAC and 3 have no corresponding scATAC at all.
How do i integrate this data?

Workflow 1

1. merge 2 multiome scATACs using merge vignette
2. merge 5 standalone scATACs using merge vignette
3. Integrate all 10 scRNA using Seurat integration
4. subset 2 multiome samples from integrated scRNA and integrate it with 2 multiome scATACs
5. subset 5 paired scRNA samples from integrated scRNA and integrate it with 5 paired scATACs
6. integrate objects if step 4 and step 5

Workflow 2

1. joint scATAC and scRNA analysis of each of the 2 samples using the multiome vignette
2. joint scATAC and scRNA analysis of each of the 5 paired sample using the cross-modality integration in the signac PBMC vignette
3. merge both multiome samples from step 1
4. merge 5 paired samples from step2
5. integrate objects from step 3 and step 4

Which would be the appropriate way to do this ?

Thanks,
Apoorva