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Cell Ranger


Loupe

10x Genomics
Chromium Single Cell Gene Expression

Cell Ranger5.0, printed on 11/23/2024

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.

MetricDescription
Custom: Number of ReadsTotal number of reads from the custom library.
Custom: Mean Reads per CellThe total number of reads from the custom library divided by the number of barcodes associated with cell-containing partitions.
Custom: Valid BarcodesFraction of reads from the custom library with a barcode found in or corrected to one that is found in the whitelist.
Custom: Sequencing SaturationFraction 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 BarcodeFraction 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 ReadFraction 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 IndexFraction 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 UMIFraction 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 ReadsFraction of reads from the custom library that contain a recognized Feature Barcode
Custom: Fraction Feature Reads UsableFraction 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 CellNumber of feature reads usable from the custom library divided by the number of cell-associated barcodes.
Custom: Fraction Unrecognized FeatureAmong 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 CellsAmong 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 CellMedian UMIs per Cell (summed over all recognized Feature Barcodes).