I want to define the identity of some cells based on a gene marker (for example the colour yellow< EYFP gene). One group of cells has the EYFP gene the other doesn't and I want to find the differential gene expression between those groups that are found on the same cell sample. Do you have any tips for a code in Seurat? Thanks
Take a look at the section "Finding Differentialy Expressed Feautres (cluster biomarkers)" of Seurat tutorial.
You have to define your clusters (if not computed automatically) by modifying the ident slot of the Seurat object.
Then you call the function FindMarkers of your Seurat object (to define markers of a given cluster against the rest) or FindAllMarkers (to look for all the combinations)