QC for Single Cell
QC for Single Cell performs quality control and removes barcodes that are deemed to not contain RNA from a single cell (for droplet-based protocols), or that are of low quality, based on different metrics. These barcodes can contribute to misleading results in the downstream analysis and should therefore be removed as a first step after the Expression Matrix has been created.
The QC for Single Cell tool can be found in the Toolbox here:
Gene Expression (
) | Cell Preparation (
) | QC for Single Cell (
)
The tool takes an Expression Matrix (
) / (
) as input.
Subsections
- Empty droplets filter
- Count-based and extra-chromosomal filters
- Doublets filter
- Interpreting the output of QC for Single Cell
- Choosing barcodes to retain
- The cell calling algorithm
- The doublet calling algorithm