splitting a Seurat object containing 2 assay types into separate Seurat objects with 1 assay each

[fudgerbeige]

Hi, I am working with a Seurat object that contain 2 assay types, RNA/Assay and ATAC/ChromatinAssay. I wanted to ask if it's possible to split this into two separate objects as I am looking to do analysis on the RNA portion separately. Thank you!

[YoukaiFromAccounting]

Hello @fudgerbeige,

To split your object into two separate objects based on assay, you can use the DietSeurat command to keep your assay of interest (make sure to set DefaultAssay beforehand):

#Split to RNA assay
DefaultAssay(obj) <- "RNA"
rna <- DietSeurat(obj, assays = "RNA")

#Split to ATAC assay
DefaultAssay(obj) <- "ATAC"
atac <- DietSeurat(obj, assays = "ATAC")

Alternatively, you can simply subset based on features from each assay, though this would keep any reductions/graphs already in the object:

rna <- subset(obj, features = rownames(obj[["RNA"]]))
atac <- subset(obj, features = rownames(obj[["ATAC"]]))

Hope this helps!

[fudgerbeige]

Thank you!