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- What is Cell Ranger?
What is Feature Barcoding?- Installation
- System Requirements
- Downloads
- Running Pipelines
- Generating FASTQs
- Specifying Input FASTQs
- Single-Sample Analysis
- Feature Barcoding Analysis
- Multi-Sample Aggregation
- Customized Reanalysis
- Map of the Pipeline
- Algorithms Overview
- Understanding Output
- Summary
- Analysis
- Matrices
- BAM
- Molecule Info
- CRISPR Outputs
- Antibody Outputs
- Metrics
- Downstream Analysis
- Using R
- Using Python
- Glossary of Terms
- Troubleshooting
10x Genomics
Chromium Single Cell Gene Expression
Cell Ranger3.0, printed on 11/14/2024
Custom Metrics
Cell Ranger supports feature-barcoding with user-defined custom features. Sequencing quality and application results metrics are provided for such custom libraries in the metrics_summary.csv file and on the web_summary.html page.
| Metric | Description |
|---|---|
Custom: Number of Reads | Total number of reads from the custom library. |
Custom: Mean Reads per Cell | The total number of reads from the custom library divided by the number of barcodes associated with cell-containing partitions. |
Custom: Valid Barcodes | Fraction of reads from the custom library with a barcode found in or corrected to one that is found in the whitelist. |
Custom: Sequencing Saturation | Fraction of reads from the custom library originating from an already-observed UMI. This is a function of library complexity and sequencing depth. More specifically, this is a ratio where: the denominator is the number of reads with a recognized Feature Barcode, valid cell-barcode, and valid UMI, and the numerator is the subset of those reads that had a non-unique combination of (cell-barcode, UMI, Feature Barcode). |
Custom: Q30 Bases in Barcode | Fraction of cell barcode bases in the custom library with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator. |
Custom: Q30 Bases in Feature Read | Fraction of feature read bases from the custom library with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator. This is Read 2 for the Single Cell 3' v3 and Single Cell 5' chemistries. |
Custom: Q30 Bases in Sample Index | Fraction of sample index bases from the custom library with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator. |
Custom: Q30 Bases in UMI | Fraction of UMI bases from the custom library with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator. |
Custom: Fraction Feature Reads | Fraction of reads from the custom library that contain a recognized Feature Barcode |
Custom: Fraction Feature Reads Usable | Fraction of reads from the custom library that contain a recognized Feature Barcode, a valid UMI, and a cell-associated barcode. |
Custom: Feature Reads Usable per Cell | Number of feature reads usable from the custom library divided by the number of cell-associated barcodes. |
Custom: Fraction Unrecognized Feature | Among all reads from the custom library for which a putative feature could be extracted, the fraction with an unrecognizable Feature Barcode |
Custom: Feature Reads in Cells | Among reads from the custom library with a recognized Feature Barcode, a valid UMI, and a valid barcode, the fraction associated with cell-containing partitions. |
Custom: Median UMIs per Cell | Median UMIs per Cell (summed over all recognized Feature Barcodes). |