dpeerlab/SEACells

Many cells have zero non-trivial (>0.1) assignments

simozhou opened this issue · 1 comments

simozhou commented

Hello,

I am running SEACells on a dataset of sc-ATAC-seq of 31000 cells and I am inferring 310 cells.

When checking for quality of results, I am surprised at the amount of cells that have 0 non-trivial assignment. Is this normal? Is there a way I can maximise the amount of cells having at least one SEACell assigned?

This is the plot I get:
SEACells_nontrivial_assignments

Thank you.

ManuSetty commented

This is quite likely a result of specifying too many metacells. We do recommend the use of one metacell for 75-80 single-cells, but this is a function of the complexity of the single-cell data. We would recommend in this case to perhaps use 150 metacells to see if it helps improve the results. A visual check on umap/visualization of your choice can also serve as a reasonable QC check.