Ambient RNA contamination occurs when droplets capture mRNA from lysed or stressed cells along with other cells. This causes:
- Cross-contamination between cell types
- Blurred cell type boundaries
- False positive marker gene expression
- Reduced clustering quality
DecontX models each cell as a mixture of two parts:
- Native transcripts from the cell's true type
- Contaminating transcripts from other cell types in the sample
We ran a benchmarking study. The table below shows the results.
| Method | Ambient RNA Removed | Precision | Conservativeness |
|---|---|---|---|
| SoupX | ~65% | High | Very conservative |
| DecontX | ~90% | Medium-High | Balanced |
| CellBender | ~90% | Medium | More aggressive |
Recommendation:
- Use SoupX when you want maximum safety and the fewest false positives.
- Use DecontX for balanced contamination removal in standard workflows.
- Use CellBender when you can replace your entire preprocessing pipeline.