How to set new identities for new clusters based on a gene expression in Seurat? I have a group of cells that have yellow (EYFP) expression and cells that don't. I want to define the yellow and non-yellow genes in two cell identities.

I clustered the cells and then created Violin Plot for EYFP expression. Then I did FindMarkers between clusters that express high EYFP with low EYFP expression. However, this is not a very accurate way to isolate cells of high and low EYFP expression. I need to use ident to separate EYFP +ve and EYFP -ve cells (but don't know the exact syntax). Then FindMarkers between these two new identities.

I need to subset a certain set of barcodes that express a marker gene (in this case Olfm4).
You have to define your ident it has to have the structure of a table. You put the cell names as names and clusters as value (for instance cell 1 = YEPF+ cell 2 = YEFP-):

pident=as.factor(clusters)
names(pident)=cellNames    
object1@ident=pident


Then you can run the FindAllMarkers function on this object:

FindAllMarkers(object1, min.pct = 0.25, min.diff.pct = 0.25)