scRNAseq Seurat conserved markers among clusters

Question

[michelafrascoli]

Hello, I am trying to find the most highly expressed genes that are conserved in all my scRNAseq clusters with Seurat.

Here is what I tried to do:

YSa.markers <- FindMarkers(object = YSa, ident.1 = 0, ident.2 = c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14), min.pct = 0.8)
print (x = head(x = YSa.markers, n = 10))

Where 0 to 14 are my clusters.

But when I make Violin plots of the genes that it gives me it’s obvious they are not expressed in all the clusters. I am clearly doing something wrong and I was wondering if anyone could help me with this.

Thank you very much for your time, Michela

Answer 1

[GouthamAtla]

Here you are trying to find markers per cluster but not genes expressed across all clusters.

You can get a list of genes that do not vary across clusters by using rowVars() function on normalised expression matrix. If the matrix is too sparse, you can average the data across similar cells by using KNN or just by pooling counts from each cluster.