QC for Single Cell
QC for Single Cell performs quality control and removes barcodes that are either deemed to not contain RNA from a single cell (Empty droplets filter and Doublets filter), or that are deemed to be of low quality, based on different metrics (Count-based and extra-chromosomal filters). These barcodes can contribute to misleading results in the downstream analysis and should 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:
Toolbox | Single Cell Analysis (
) | Gene Expression (
) | Cell Preparation (
) | QC for Single Cell (
)
The tool takes an Expression Matrix (
) / (
) as input.
|
Batches and samples: The distribution of the QC metrics can vary between batches. Therefore, QC for Single Cell analyzes each batch separately by treating each sample detected in the input Expression Matrix as a different batch. This might not be appropriate for samples that are sequenced together in one batch, as can be the case for Parse Biosciences data, see Demultiplex Parse Bio Samples, or multiplexed samples, see Update Single Cell Sample Name. For such data, we recommend running QC for Single Cell before updating the sample name. |
Subsections
- Empty droplets filter
- Count-based and extra-chromosomal filters
- Doublets filter
- The output of QC for Single Cell
- Choosing barcodes to retain
- Cell calling
- Automatic thresholds
- Doublet calling