Output FindMarkers()

Question

[Chris]

Hi all,

Would you please share why I got peaks instead of genes when using this command:

compare_0 <- FindMarkers(merged_seurat, ident.1 = 'WT_0', ident.2 = 'MT_0')
head(compare_0)

Thank you so much!

Answer 1

[bk11]

Hey, it looks like you are doing scATAC-seq data analysis. Here you are checking for Differentially accessible peaks between cell types.

[Chris]

Hi bk11, I am doing single cell multiome RNA + ATAC but I only read RNA assay into RStudio to analyze first.

[bk11]

You need to change the default assays before running FindMarkers then-

#To find markers in your RNA data slot
DefaultAssay(merged_seurat) <- "RNA"
compare_0 <- FindMarkers(merged_seurat, ident.1 = 'WT_0', ident.2 = 'MT_0')

#To find markers in your ATAC data slot
DefaultAssay(merged_seurat) <- "ATAC"
compare_0 <- FindMarkers(merged_seurat, ident.1 = 'WT_0', ident.2 = 'MT_0')

[Chris]

Unfortunately, it doesn't work as you see the only assay I have in this case is RNA.

[bk11]

Then your upstream steps of FindMarkers are off. I would make sure I read the correct data.

[Chris]

I used Readmtx() to read 3 files: matrix, feature and barcode. The file filtered_feature_bc_matrix.h5 will have ATAC seq assay but I didn't run.