Splitting scRNA seq data from Multiome data(scRNA+ scATAC)
1
0
Entering edit mode
10 months ago

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.

scRNA-seq Signac • 743 views
ADD COMMENT
2
Entering edit mode
10 months ago
bk11 ★ 3.0k

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(scRNAseq@meta.data)
                      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
ADD COMMENT
0
Entering edit mode

Thank you so much!

ADD REPLY
1
Entering edit mode

A small educational note: if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they work. This will help future users that might find this post find the right answer.

upvote_bookmark_accept

ADD REPLY

Login before adding your answer.

Traffic: 1105 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6