Combining RNA and ATAC

Question

[francesca3]

Hi, I'm trying to make a joint analysis of RNA and ATAC data but I'm having troubles. I have 6 datasets of RNA and 4 of ATAC. This is what I tried to do

1.Integration of RNA datasets using SCT transformation v2 2.Integration of ATAC following the standard pipeline vignette

The problem comes when I want to merge the two modalities to go through WNN analysis.

I tried merging the two integrated datasets with the merge function and it appears a warning

“Attempting to merge an SCTAssay with another Assay type Converting all to standard Assay objects.”

So, when I call FindMultiModalNeighbors, this error comes out :

Error: Cannot find 'pca' in this Seurat object

Basically, I think that the PCA slot of SCT assay is removed.

What can I do?

Thanks Francesca

[bioinformatics.girl]

There's a number of multiomic analyses pipelines on Github; have you referred to those?