Table 1 Summary of QC survey
From: Biology-inspired data-driven quality control for scientific discovery in single-cell transcriptomics
Metric\QC type | Papers with any QC | Data-agnostic fixed threshold (% of filtered) | Multiple fixed thresholds varying by sample | Mito or ribo genes removed before analysis | Data-driven study-level threshold | Custom QC | No filtering |
|---|---|---|---|---|---|---|---|
nCounts | 65 | 48 (73.8%) | 5 (7.7%) | 0 (0%) | 11 (16.9%) | 1 (1.5%) | 42 |
nGenes | 89 | 72 (80.8%) | 5 (5.6%) | 0 (0%) | 12 (13.5%) | 0 (0%) | 18 |
nCells | 41 | 35 (85.4%) | 3 (7.3%) | 0 (0%) | 2 (4.9%) | 1 (2.4%) | 65 |
%Mito | 85 | 69 (81.2%) | 5 (5.9%) | 4 (4.7%) | 6 (7.1%) | 1 (1.2%) | 22 |
%Ribo | 7 | 2 (28.6%) | 0 (0%) | 3 (42.8%) | 2 (28.6%) | 0 (0%) | 100 |
Empty droplets | Doublets/multiplets | Ambient RNA | |||||
4 | 17 | 6 | |||||