integrating snRNA (from multiome dataset) with scRNA public dataset

[Urja25]

Hi,

I tried integrating three PBMC snRNAseq data from 10X Genomics multiome datasets with two scRNA seq data from a 10X Genomics Public dataset. However, all the data from the multiome clusters separately from the scRNAseq data. How can I remove batch effects in this case?

Thanks a lot!

[pati-ni]

Are you using only snRNAseq? Is everything PBMC? Can you provide a walkthrough of your analysis?