Entering edit mode
2.9 years ago
firestar
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This is the summary from the CellRanger run showing ~150,000 reads per cell.
But, when I read the results into R, I get only ~5000 reads per cell. This is before any pre-filtering in Seurat.
x <- Seurat::Read10X_h5("data/PBMC_1_3_1/count/sample_feature_bc_matrix.h5")$`Gene Expression`
hist(colSums(x))
median(colSums(x))
[1] 5050.5
This is a huge difference and I wonder if I am making a mistake somewhere.
Ah right! I knew I was overlooking something obvious. Thanks!
Yeah, 10xGenomics cheats a little by displaying the total reads far more prominently than the value you really want, the # of UMIs.