Splitting scRNA seq data from Multiome data(scRNA+ scATAC)

Question

[gradstudent]

Could anyone help me with splitting the scRNA seq data from a Multiome dataset (scATAC + snRNA seq). I'm trying to create a separate anndata from the scRNA seq portion only.

I've tried setting the Default using Signac as RNA and then saving the rds file, but I don't think that works.

Answer 1

[bk11]

You can do split the multiome data in following way-

#Your Multiome data
pbmc
An object of class Seurat 
142657 features across 11909 samples within 2 assays 
Active assay: RNA (36601 features, 0 variable features)
 1 layer present: counts
 1 other assay present: ATAC

#Splitting the scRNA seq data from multiome data
scRNAseq <- CreateSeuratObject(counts = pbmc@assays$RNA)
head([e-mail])
                      orig.ident nCount_RNA nFeature_RNA
AAACAGCCAAGGAATC-1 SeuratProject       8380         3308
AAACAGCCAATCCCTT-1 SeuratProject       3771         1896
AAACAGCCAATGCGCT-1 SeuratProject       6876         2904
AAACAGCCACACTAAT-1 SeuratProject       1733          846
AAACAGCCACCAACCG-1 SeuratProject       5415         2282
AAACAGCCAGGATAAC-1 SeuratProject       2759         1353

scRNAseq
An object of class Seurat 
36601 features across 11909 samples within 1 assay 
Active assay: RNA (36601 features, 0 variable features)
 1 layer present: counts

[gradstudent]

Thank you so much!

[Ram]

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