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Hi, I was wondering whether we can find the differentially expressed genes between the Double-KO and the Shox2-KO. For the FindMarker() function, only see the differential expressed gene between different identities. I don't know whether we can find the differential expressed gene between only these two samples.

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If I understand your question correctly, you can simply use SetIdent() to change the "default identity" to your samples and then use FindMarker() with the ident.1 = "Double-KO" and ident.2 = "Shox2-KO".

Alternatively, you can "collapse" or "summarize" your single cell data into a pseudo-bulk and then use one of the bulk RNA-seq packages.

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  • $\begingroup$ Hi haci, that is a good idea. But I have tried to look the script of SetIdent(), find some difficulties to do it. Can you please give me more detail? $\endgroup$
    – hua
    Commented Dec 28, 2019 at 17:31
  • $\begingroup$ You can set the ident.use parameter of SetIdent() function to one of the columns in your meta.data slot of your Seurat object. $\endgroup$
    – haci
    Commented Dec 28, 2019 at 20:46
  • $\begingroup$ I'm not sure this is right. SetIdent is used to assign new ident information; you give it a vector of cells to tag. All you want to do is change the active ident that FindMarkers will use, and you do that with Ident(). $\endgroup$
    – swbarnes2
    Commented Sep 23, 2020 at 17:37

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