Problems in RNA and ATAC combination after SCT transformation on RNA data

[francescasci91]

Hi, I'm trying to combine RNA and ATAC data .I have 6 datasets of RNA and 4 datasets of ATAC. I decided to proceed in this way, also following what posted here satijalab/seurat#5346:

1. integration of RNA datasets (using SCT transformation v2)
2. integration of ATAC datasets using the standard pipeline
3. combine the two integrated datasets obtained in point 1 and 2 to run WWN analysis.

I'm having problems with the third point.

When I try to use the merge function I obtain this warning
“Attempting to merge an SCTAssay with another Assay type Converting all to standard Assay objects.”

And then when I try to run PCA
Error: Cannot find 'pca' in this Seurat object

Do you have any suggestion how to solve this??

How can I merge the two objects?

Thanks
Francesca

[timoast]

If you have separate RNA and ATAC datasets that you want to integrate, you can follow the steps shown here: https://satijalab.org/signac/articles/pbmc_vignette.html#create-a-gene-activity-matrix-1

WNN is not appropriate here, that method is designed for datasets where both modalities are measured in the same cell.

[francescasci91]

And if I have 4 Multiome + 2 RNA datasets, it is still advisable to use the pipeline reported here #1012 ?
So also in that case I cannot use WWN analysis but gene activity to transfer labels?
Thanks
Francesca

[timoast]

For integrating multiome and scRNA, there's no need to use gene activities since all the datasets have RNA measured already

[nmrecka]

The link above is broken. Is there an update version of this vignette somewhere else?

[timoast]

https://stuartlab.org/signac/articles/pbmc_vignette#create-a-gene-activity-matrix