Getting the cells from the clusters Seurat has found
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2.7 years ago
suvratha ▴ 60

Hello, I've been using Seurat v3.1 for single-cell analysis of mouse data. I've clustered the cells and Seurat has found 12 different clusters for my data. Now, I need to name the clusters so that I know which particular cell type has clustered where on the UMAP plot. Is there any other way to do this other than using the FindMarkers() function and then naming them based on the most differentially expressed gene in the cluster? Also, is there a way to retrieve the data where we know which cell/data has gone into the UMAP predicted cluster so that I can at least I know which cell type has gone where in the plot based on a metadata file I have for my data?

Thank you.

RNA-Seq Seurat single cell R • 2.2k views
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you can plot the known marker gene to check the cluster.

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2.6 years ago
Evan ▴ 170

Hello, I got approximately the same question recently and I succeed to find the answer. Here is the command in Seurat to get a file with two columns, one with cell sequence and a second column with associated cluster. Each line of this file will be one cell.

write.table(yourdata@active.ident, file='Cell_Cluster.tsv', quote=FALSE, sep='\t', col.names = FALSE)
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