10x Genomics Support/Cell Ranger 7.2/Analysis/

Antibody Metrics Outputs from the Cell Ranger Pipelines

Cell Ranger computes sequencing quality and application results metrics on each supported library, which currently are Antibody Capture, CRISPR Guide Capture, and Custom (user-defined assays that are neither Antibody nor CRISPR). These metrics will be computed and displayed only when one of these library types was used. This page describes Antibody Capture libraries metrics for QC of the library prep and sequencing of antibody libraries, which appear in the metrics_summary.csv file and on the web_summary.html page.

MetricDescription
Antibody: Number of ReadsTotal number of reads.
Antibody: Mean Reads per CellThe total number of reads divided by the number of barcodes associated with cell-containing partitions.
Antibody: Valid BarcodesFraction of reads with a cell-barcode found in or corrected to one that is found in the whitelist.
Antibody: Fraction Antibody Reads in Aggregate BarcodesFraction of reads lost after removing aggregate barcodes.
Antibody: Sequencing SaturationFraction of antibody library reads 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 antibody 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, antibody barcode).
Antibody: Q30 Bases in BarcodeFraction of cell barcode bases with Q-score greater than or equal to 30, excluding very low quality/no-call (Q less than or equal to 2) bases from the denominator.
Antibody: Q30 Bases in Antibody ReadFraction of bases from the read containing the antibody barcode with Q-score greater than or equal to 30, excluding very low quality/no-call (Q less than or equal to 2) bases from the denominator. This is Read 2 for the Single Cell 3' v3 and Single Cell 5' chemistries.
Antibody: Q30 Bases in Sample IndexFraction of sample index bases with Q-score greater than or equal to 30, excluding very low quality/no-call (Q less than or equal to 2) bases from the denominator.
Antibody: Q30 Bases in UMIFraction of UMI bases with Q-score greater than or equal to, excluding very low quality/no-call (Q less than or equal to 2) bases from the denominator.
Antibody: Fraction Antibody ReadsFraction of reads that contain a recognized antibody barcode
Antibody: Fraction Antibody Reads UsableFraction of reads that contain a recognized antibody barcode, a valid UMI, and a cell-associated barcode.
Antibody: Antibody Reads Usable per CellNumber of antibody reads usable divided by the number of cell-associated barcodes.
Antibody: Fraction Unrecognized AntibodyAmong all reads, the fraction with an unrecognizable antibody barcode
Antibody: Antibody Reads in CellsAmong reads with a recognized antibody barcode, a valid UMI, and a valid barcode, the fraction associated with cell-containing partitions.
Antibody: Median UMIs per CellMedian UMIs per Cell (summed over all recognized antibody barcodes).
Antibody: Fraction antibody reads in aggregate barcodesFraction of read pairs that were lost due to the removal of barcodes containing aggregates.
Antibody: Valid UMIsFraction of reads with valid UMIs; i.e. UMI sequences that do not contain Ns and that are not homopolymers.
Antibody: Number of Short Reads SkippedTotal number of read pairs that were ignored by the pipeline because they do not satisfy the minimum length requirements (for example Read-1 less that 26 bases in 3' v2 or 3' v3 or 5').