Identifying DEG's on Integrated samples
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21 days ago
cgp09741 ▴ 10

Hello,

I am analyzing snRNA-seq data that is composed of a KO and WT sample. I have integrated/anchored and clustered the two datasets to identify similarities and differences across the two samples. I have identified the DEGs for each cluster of each sample independently using FindMarkers... But beyond this we would like to generate a list of DEGs for each cluster that compares the KO and WT in order to identify the differences our KO is causing. Is there a function to specifically look at DEGs between samples in specific clusters?

Seurat DEG • 237 views
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https://nbisweden.github.io/workshop-scRNAseq/labs/compiled/scanpy/scanpy_05_dge.html for "Differential expression across conditions" with few lines of code to identify DEGs per cluster.

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Entering edit mode
5 days ago
AB ▴ 330

You can add a new column to your meta data and use that column to run FindMarkers again

seuratobj@meta.data$new_column = paste0(seuratobj@meta.data$sample_name,"_",seuratobj@meta.data\$cluster,sep="")
Idents(seuratobj) = "new_column"
deg = FindAllMarkers(seuratobj)