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

Hello,

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 group.by in FindMarkers but not worked.

Thanks.

scRNA-SEQ NGS rna-seq • 352 views
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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 seurat@meta.data 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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