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  • how to calculate DEG in a certain cluster using Seurat

    I am a new user of Seurat, and I'd like to know how to correctly calculate the DEG from a certain cluster/sub-population?

    Here are some basic description about the data I have and steps I use -
    Samples: 3 control samples and 3 case/disease samples
    Steps:
    1) In the first several steps, I used FindVariableFeatures() followed by FindIntegrationAnchors(...anchor.features = 1000...) and IntegrateData() to make a Seurat object (1000 gene x 36000 cells from 3+3 samples)
    2) In the next steps, I got the 11 clusters in the tsne plot
    3) subset() to get the cells in a Cluster1, and Idents(Cluster1)[email protected]$Group to divide case and control
    4) Then shall I used a) or b) or some other method to calculate DEG?
    a) deg_1000 <- FindMarkers(hsc, ident.1 = "ctrl", ident.2 = "case", verbose = FALSE)
    b) deg_all <- FindMarkers(hsc, ident.1 = "ctrl", ident.2 = "case", verbose = FALSE, assay="RNA")
    As in a) the max number of genes I have is 1000, but from the original assay "RNA", I have totally ~20K genes, for which I want to know the pattern of gene expression changes.

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