Cell Ranger2.0, printed on 12/21/2024
Cell Ranger pipelines output key metrics in text format. Below are the definitions of the reported metrics.
The cellranger vdj pipeline outputs metrics_summary.csv which contains a number of key metrics about the barcoding and sequencing process.
| Type | Name | Description |
|---|---|---|
| int | Estimated Number of Cells | The number of barcodes estimated to be associated with cells that express targeted V(D)J transcripts. A barcode is cell-associated if it has a contig with at least 2 UMIs with sufficient read support. |
| int | Mean Read Pairs per Cell | Number of input read pairs divided by the estimated number of cells. |
| int | Number of Cells With Productive V-J Spanning (TRA, TRB) Pair | Number of cell barcodes for which at least 1 sequence was found for each of TRA and TRB. Both sequences must have an annotated CDR3, must be predicted to be productive, and must span the beginning of the 5′ end of the V region to the 3′ end of the J region. |
| int | Number of Read Pairs | Total number of read pairs that were assigned to this library in demultiplexing. |
| float | Valid Barcodes | Fraction of reads with barcodes that match the whitelist after barcode correction. |
| float | Q30 Bases in Barcode | Fraction of cell barcode bases with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator. |
| float | Q30 Bases in RNA Read 1 | Fraction of RNA read 1 bases with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator. |
| float | Q30 Bases in RNA Read 2 | Fraction of RNA read 2 bases with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator. |
| float | Q30 Bases in Sample Index | Fraction of sample index bases with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator. |
| float | Q30 Bases in UMI | Fraction of UMI bases with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator. |
| float | Reads Mapped to Any V(D)J Gene | Fraction of reads that partially or wholly map to any germline V(D)J gene segment. |
| float | Reads Mapped to TRA | Fraction of reads that map partially or wholly to a germline TRA gene segment. |
| float | Reads Mapped to TRB | Fraction of reads that map partially or wholly to a germline TRB gene segment. |
| int | Mean Used Read Pairs per Cell | Mean number of read pairs used in assembly per cell-associated barcode. These reads must have a cell-associated barcode, map to a V(D)J gene, and have a UMI with sufficient read support. This value is counted after subsampling to a fixed N50 reads per UMI (See Assembly Subsampling Rate). |
| float | Assembly Subsampling Rate | Fraction of usable (assemblable) reads retained for assembly. The assembler uniformly subsamples reads to achieve a target N50 reads per UMI. If multiple gem groups were given as input, this is the weighted average across all gem groups, where each gem group is weighted by its total number of reads with a valid barcode and UMI. |
| float | Fraction Reads in Cells | Number of reads with cell-associated barcodes divided by the number of reads with valid barcodes. |
| float | Median TRA UMIs per Cell | Median number of UMIs assigned to a TRA contig per cell. |
| float | Median TRB UMIs per Cell | Median number of UMIs assigned to a TRB contig per cell. |
| float | Paired Clonotype Diversity | Effective diversity of the paired clonotypes, computed as the Inverse Simpson Index of the clonotype frequencies. A value of 1 indicates a minimally diverse sample - only one distinct clonotype was detected. A value equal to the estimated number of cells indicates a maximally diverse sample. |
| float | Cells With TRA Contig | Fraction of cell-associated barcodes with at least one TRA contig annotated as a full or partial V(D)J gene. |
| float | Cells With TRB Contig | Fraction of cell-associated barcodes with at least one TRB contig annotated as a full or partial V(D)J gene. |
| float | Cells With CDR3-annotated TRA Contig | Fraction of cell-associated barcodes with at least one TRA contig where a CDR3 was detected. |
| float | Cells With CDR3-annotated TRB Contig | Fraction of cell-associated barcodes with at least one TRB contig where a CDR3 was detected. |
| float | Cells With V-J Spanning Contig | Fraction of cell-associated barcodes with at least one contig spanning the 5′ end of the V region and the 3′ end of the J region. |
| float | Cells With V-J Spanning TRA Contig | Fraction of cell-associated barcodes with at least one contig spanning the 5′ end of the V region and the 3′ end of the J region for TRA. |
| float | Cells With V-J Spanning TRB Contig | Fraction of cell-associated barcodes with at least one contig spanning the 5′ end of the V region and the 3′ end of the J region for TRB. |
| float | Cells With Productive TRA Contig | Fraction of cell-associated barcodes with at least one contig that spans the 5′ end of the V region and the 3′ end of the J region for TRA, has a start codon in the expected part of the V sequence, has an in-frame CDR3, and has no stop codons in the V-J region. |
| float | Cells With Productive TRB Contig | Fraction of cell-associated barcodes with at least one contig that spans the 5′ end of the V region and the 3′ end of the J region for TRB, has a start codon in the expected part of the V sequence, has an in-frame CDR3, and has no stop codons in the V-J region. |
| float | Cells With Productive V-J Spanning (TRA, TRB) Pair | Fraction of cell-associated barcodes with at least one contig for each chain of the receptor pair satisfying the following: the contig annotations span the 5′ end of the V region and the 3′ end of the J region of the chain, a start codon was found in the expected part of the V sequence, an in-frame CDR3 amino acid motif was found, and no stop codons were found in the V-J region. |
| float | Contigs Unannotated | Fraction of assembled contigs not annotated with any V(D)J gene. |