Cell Ranger7.1, printed on 12/21/2024
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.
| Metric | Description |
|---|---|
CRISPR: Number of Reads | Total number of reads from the CRISPR library. |
CRISPR: Mean Reads per Cell | The total number of reads from the CRISPR library divided by the number of barcodes associated with cell-containing partitions. |
CRISPR: Valid Barcodes | Fraction of reads from the CRISPR library with a cell-barcode found in or corrected to one that is found in the whitelist. |
CRISPR: Sequencing Saturation | Fraction 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 Barcode | Fraction 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 Read | Fraction 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 Index | Fraction 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 UMI | Fraction 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 | 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 Reads | Fraction of reads from the CRISPR library with a recognized protospacer sequence. |
CRISPR: Fraction Guide Reads Usable | Fraction of reads from the CRISPR library with a recognized protospacer sequence, a valid UMI, and a cell-associated barcode. |
CRISPR: Guide Reads Usable per Cell | Number of guide reads usable divided by the number of cell-associated barcodes. |
CRISPR: Fraction Protospacer Not | 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 Cells | Among 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 | Cells identified by the protospacer-calling algorithm as expressing 1 or more protospacers. |
CRISPR: Cells with 2 or more | Cells identified by the protospacer-calling algorithm as expressing 2 or more protospacers. |
CRISPR: Median UMIs per Cell | Median UMIs per Cell (summed over all recognized protospacers). |
CRISPR: Valid UMIs | Fraction of reads with valid UMIs; i.e. UMI sequences that do not contain Ns and that are not homopolymers. |
CRISPR: Number of Short Reads Skipped | Total 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'). |