Table 1. Overview of the aggregated number of cells across samples removed at each step of the quality control (QC) as part of scFlow.
Note that cells can fail QC for more than one check, so only the total failed and total passed rows will sum to 100%.
| QC steps | Total cells | Percentage |
|---|---|---|
| Pre-QC | 35,389,440 | |
| Total failed | 35,337,874 | 99.85 |
| Minimum library size (n < 200) | 35,307,281 | 99.77 |
| Maximum library size | 4742 | 0.01 |
| Minimum expressed genes (n < 200) | 35,312,434 | 99.78 |
| Maximum library size/expressed genes (MAD> 4) | 2149 | 0.01 |
| Proportion of mitochondrial genes (≥ 0.1) | 1,097,738 | 3.10 |
| Multiplets (pK = 0.0054) | 581 | 0.00 |
| Total passed | 51,566 | 0.15 |
MAD, median absolute deviation.