How to generate Cluster annotation file

[husain223]

I wanted to generate a Cluster annotation file that includes the barcode and another one cluster column, so how can I add a clustered column in the barcode tsv file?

[2019surbhi]

If you have already added cell type annotation as in metadata column of your Seurat object, you can use the following code:

Extract cell type annotation
meta_dat<-as.data.frame(obj@meta.data$cell_type)

Add barcodes as 1st column to this table
meta_dat<-cbind(rownames(obj@meta.data),meta_dat)
rownames(meta_dat)<-NULL

Save table in current directory (or change the code to add it to desired output directory)

write.table(x = meta_dat,
file = 'project1_cell_type_annotation.txt'),
sep = '\t', row.names = F, col.names = F, quote = F)