Cell Ranger3.0, printed on 12/17/2024
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. |
| 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 (see the Assembly section). |
| 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 full-length contig. |
| float | Cells With V-J Spanning TRA Contig | Fraction of cell-associated barcodes with at least one full-length TRA contig. |
| float | Cells With V-J Spanning TRB Contig | Fraction of cell-associated barcodes with at least one full-length TRB contig. |
| float | Cells With Productive TRA Contig | Fraction of cell-associated barcodes with at least one full-length TRA contig, 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 full-length TRB contig, 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 are full-length, 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. |
| float | Cell Count Confidence | Fraction of cell barcodes that have been very confidently called as cells. This indicates the quality of the separation between background and cell-associated barcodes. |