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10x Genomics
Chromium Single Cell Gene Expression

CRISPR Metrics

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 in the assay. This page describes CRISPR library metrics for QC of the library prep and sequencing of CRISPR libraries, which appear in the metrics_summary.csv file and on the web_summary.html page.

MetricDescription
CRISPR: Number of ReadsTotal number of reads from the CRISPR library.
CRISPR: Mean Reads per CellThe total number of reads from the CRISPR library divided by the number of barcodes associated with cell-containing partitions.
CRISPR: Valid BarcodesFraction of reads from the CRISPR library with a cell-barcode found in or corrected to one that is found in the whitelist.
CRISPR: Sequencing SaturationFraction of CRISPR 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 protospacer sequence, 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, protospacer sequence).
CRISPR: Q30 Bases in BarcodeFraction of cell barcode bases from the CRISPR library with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator.
CRISPR: Q30 Bases in RNA ReadFraction of bases from the read containing the protospacer 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.
CRISPR: Q30 Bases in Sample IndexFraction of sample index bases from the CRISPR library with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator.
CRISPR: Q30 Bases in UMIFraction of UMI bases in the CRISPR library with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator.
CRISPR: Fraction Reads with Putative
Protospacer Sequence
Fraction of reads from the CRISPR library from which a putative protospacer sequence could be extracted, as per the patterns specified in the Feature Definition File. For example, if the specified pattern is "20 bases upstream of sequence X", this metric specifies the fraction of reads containing sequence X and 20 bases upstream of it.
CRISPR: Fraction Guide ReadsFraction of reads from the CRISPR library with a recognized protospacer sequence.
CRISPR: Fraction Guide Reads UsableFraction of reads from the CRISPR library with a recognized protospacer sequence, a valid UMI, and a cell-associated barcode.
CRISPR: Guide Reads Usable per CellNumber of guide reads usable divided by the number of cell-associated barcodes.
CRISPR: Fraction Protospacer Not
Recognized
Among all reads from the CRISPR library from which a putative protospacer sequence could be extracted, the fraction with a protospacer sequence that was not recognized.
CRISPR: Guide Reads in CellsAmong reads from the CRISPR library with a recognized protospacer sequence, a valid UMI, and a valid barcode, the fraction associated with cell-containing partitions.
CRISPR: Cells with 1 or more
protospacers detected
Cells identified by the protospacer-calling algorithm as expressing 1 or more protospacers.
CRISPR: Cells with 2 or more
protospacers detected
Cells identified by the protospacer-calling algorithm as expressing 2 or more protospacers.
CRISPR: Median UMIs per CellMedian UMIs per Cell (summed over all recognized protospacers).