How to compare two Seurat object (sample) in order to find top markers?
Entering edit mode
6 weeks ago
ahmad mousavi ▴ 550


I have merged two Seurat object, they are not technical replicate, in fact they are different sample types. I have done integration using IntegrateData function in Seurat4.

I have a question, how can I find top markers between two Seurat object, because they seems not really close even in phenotype, and worth to find their top markers.

I have put label for each sample and try to use in FindMarkers but not worked.


scRNA-SEQ NGS rna-seq • 352 views
Entering edit mode
25 days ago
Ondina ▴ 30

I'm not sure I completely understand your question but I suggest your merge your two Seurat objects with the following command:

merged <- merge(seurat1, seurat2, add.cell.ids = c("seurat1", "seurat2"), project = "merged_seurat")

Then, the information between which original seurat object are the cells coming from will be stocked in the in the orig.ident column.

You can rename your idents as your orig.ident in order to use your FindMarkers function:

Idents(object = merged) <- "orig.ident"

And then run:

markers_seurat1_vs_seurat2 <- FindMarkers(merged, ident.1 = "seurat1, ident.2 = "seurat2", method = "DESeq2")

(and choose the method you want)

Here's more information:

Seurat Cheat Sheet

Find markers by orig.ident


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