Question: Estimated Number of Cells in 10X vs Cells in Seurat
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gravatar for Payal
6 weeks ago by
Payal90
Payal90 wrote:

Hi,

Why the "Estimated Number of Cells" and when I do dim(seurat_object) have different number of cells?

10X defines "Estimated Number of Cells" as "The number of barcodes associated with cell-containing partitions, estimated from the barcode UMI count distribution."

Eg:My sample in 10X summary report says "Estimated Number of Cells" is 8,388. However when I load the object in Seurat and do dim(seurat_object), I get 53847 cells.

What am I missing?

Thanks, Payal

sequencing R single-cell • 151 views
ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by Payal90

Ok...show us how exactly you are loading your data into Seurat.

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by swbarnes28.6k

I did this:

sample1 <- Read10X("~/../outs/raw_feature_bc_matrix")

sample1_seurat <- CreateSeuratObject(counts = sample1, 
                                    min.cells = 3, 
                                    min.features = 200, 
                                    project = "sample1")

This should reduce the number of cells and genes instead the numbers don't seem to match

ADD REPLYlink written 6 weeks ago by Payal90
1

What happens if you use filtered instead of raw?

ADD REPLYlink written 6 weeks ago by swbarnes28.6k

Thanks a ton! Yes "filtered_feature_bc_matrix" makes sense and the numbers match.

ADD REPLYlink written 6 weeks ago by Payal90
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