Identifying DEG's on Integrated samples

Question

[cgp09741]

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?

Thank you for your help.

[Omics data mining]

You can follow given link
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.

Answer 1

[AB]

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

[e-mail]$new_column = paste0([e-mail]$sample_name,"_",[e-mail]$cluster,sep="")
Idents(seuratobj) = "new_column"
deg = FindAllMarkers(seuratobj)