cell type identification

[lvweiming]

I have 20 clusters. but only 5 of them have cell-type identification after running with scCATCH. other still showing clusters number instead of the cell type.
Can anyone tell what could be reasons and how to fix it?

[multitalk]

Hello, there are two solutions you can try.

(1) Adjust the parameters in findmarkergenes() by setting a lower cell_min_pct and logfc, e.g., cell_min_pct = 0.1, logfc = 0.1, and run scCATCH() again.

clu_markers <- findmarkergenes(Seurat_object,cell_min_pct = 0.1, logfc = 0.1)
clu_ann <- scCATCH(clu_markers)

(2) Use FindAllMarkers() of Seurat, and run scCATCH() again.

clu_markers <- FindAllMarkers(Seurat_object)
clu_ann <- scCATCH(clu_markers)

[lvweiming]

Hello, there are two solutions you can try.

(1) Adjust the parameters in findmarkergenes() by setting a lower cell_min_pct and logfc, e.g., cell_min_pct = 0.1, logfc = 0.1, and run scCATCH() again.

clu_markers <- findmarkergenes(Seurat_object,cell_min_pct = 0.1, logfc = 0.1)
clu_ann <- scCATCH(clu_markers)

(2) Use FindAllMarkers() of Seurat, and run scCATCH() again.

clu_markers <- FindAllMarkers(Seurat_object)
clu_ann <- scCATCH(clu_markers)

[lvweiming]

Hello, there are two solutions you can try.

(1) Adjust the parameters in findmarkergenes() by setting a lower cell_min_pct and logfc, e.g., cell_min_pct = 0.1, logfc = 0.1, and run scCATCH() again.

clu_markers <- findmarkergenes(Seurat_object,cell_min_pct = 0.1, logfc = 0.1)
clu_ann <- scCATCH(clu_markers)

(2) Use FindAllMarkers() of Seurat, and run scCATCH() again.

clu_markers <- FindAllMarkers(Seurat_object)
clu_ann <- scCATCH(clu_markers)

Thank you for answer my question. the second method solves my problem.