I am processing the same dataset with both Seurat and Scanpy. In Seurat, I got 3 clusters and cluster 2 seems like the target cell type; I got 2 clusters in Scanpy and cluster 1 seems like the target. I am trying to get the marker genes that shows up in both target clusters. But I have two questions...
My understanding is that if I didn't specify ident.2 in Seurat's "FindMarkers", Seurat will find the marker genes comparing the ident.1=0 to the rest, am I right? If so, what's the difference between FindMarkers(object = dataa, ident.1 = 2, min.pct = 0.25), FindMarkers(object = dataa, ident.1 = 2, ident.2 = c(0, 1), min.pct = 0.25) and FindAllMarker(object=dataa, min.pct=0.25)?
Since I'm comparing Seurat result with Scanpy's "sc.tl.rank_genes_groups", which processing method in question 1 should I compare with?
I'm really confused, it would be helpful if someone can explain these to me.
Thank you so much!