Merging and Integrating Preprocessed GEX to ATAC (10X Multiome)

[AAA-3]

Cross posting:

Hello,

I have a question about the computational order of operations that I have:

I have 10X Multiome experiments (8 samples) of ATAC and GEX. I already merged, integrated, clustered etc. my 8 GEX runs into one seurat object to analyse GEX in one assay Now I want to add in the ATAC data to commence these analyses

Based on the vignette, I get the impression that we should add the chromatin assay of each of our 8 samples individually prior to the integrated analysis. Would there be a way for me to add them to my integrated GEX data without starting from scratch? I am not sure how to add them in with all the layers that my Seurat Object has at the moment.

Thanks in advance!

Originally posted by @AAA-3 in https://github.com/satijalab/seurat/discussions/8672