Entering edit mode
16 months ago
Chris
▴
340
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!
Hi bk11, I am doing single cell multiome RNA + ATAC but I only read RNA assay into RStudio to analyze first.
You need to change the default assays before running
FindMarkers
then-Unfortunately, it doesn't work as you see the only assay I have in this case is RNA.
Then your upstream steps of
FindMarkers
are off. I would make sure I read the correct data.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.