Problem statement:
Most pipelines remove cells below a fixed total count threshold. However, some cell types, e.g. T-cells, have less mRNA than others, e.g. tumor cells. Thus total counts filters remove say the lowest expressing 10% of tumor cells, but the lowest expressing 30% of T-cells, returning a biased census of the cell type landscape.
Proposed work:
- Investigate how profound this bias is. Describe which analyses are robust vs. sensitive to this bias.
- Propose a QC filter that removes cells from different cell types at approximately the same rate.
Problem statement:
Most pipelines remove cells below a fixed total count threshold. However, some cell types, e.g. T-cells, have less mRNA than others, e.g. tumor cells. Thus total counts filters remove say the lowest expressing 10% of tumor cells, but the lowest expressing 30% of T-cells, returning a biased census of the cell type landscape.
Proposed work: