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

[NadiaEdel]

Hi! I would love to know the answer to this or if you were able to figure it out.
I have 9 multiome (RNA+ATAC from same cell) datasets, and I am struggling to figure out how to process them all, ended up with the same "two workflows" as suggested by mengm5.

Any tips are much appreciated!

Thank you!

Nadia

[bapoorva]

Hi !

I would love to know this as well. In fact, my dataset a bit more complicated. I have 40 samples - 8 are multiome (scrna+scatac),22 are standalone scrna and scatac on same samples and 10 do not have atac information at all. I have finished the analysis on my scrna and i have integrated datasets that are annotated. I'm really confused on how to approach this.

Apoorva