Cell Ranger3.1, printed on 12/26/2024
The cellranger vdj pipeline outputs metrics_summary.csv which contains a number of key metrics about the barcoding and sequencing process. Conventions for these metrics:
| Type | Name | Description |
|---|---|---|
| int | Estimated Number of Cells | The number of barcodes estimated to correspond to GEMs containing cells. See Targeted Cell Calling Algorithm. |
| 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 Pair | Number of cell barcodes for which at least one productive sequence was found for each of TRA and TRB (or heavy and light chains, for Ig). |
| 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. |
| float | Q30 Bases in RNA Read 1 | Fraction of read 1 bases with Q-score ≥ 30. (Likewise for read 2.) |
| float | Q30 Bases in Sample Index | Fraction of sample index bases with Q-score ≥ 30. |
| float | Q30 Bases in UMI | Fraction of UMI bases with Q-score ≥ 30. |
| float | Reads Mapped to Any V(D)J Gene | Fraction of reads that partially or wholly map to a V(D)J gene segment. |
| float | Reads Mapped to TRA | Fraction of reads that map partially or wholly to a TRA gene segment. |
| int | Mean Used Read Pairs per Cell | Mean number of read pairs used in assembly per cell barcode. These reads must have a cell barcode, map to a V(D)J gene, and have a UMI with sufficient read support, counted after subsampling. |
| float | Fraction Reads in Cells | Number of reads with cell 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 | 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 barcodes with at least one TRA contig annotated as a full or partial V(D)J gene. |
| float | Cells With CDR3-annotated TRA Contig | Fraction of cell barcodes with at least one TRA contig where a CDR3 was detected. |
| float | Cells With V-J Spanning Contig | Fraction of cell barcodes with at least one full-length contig. |
| float | Cells With V-J Spanning TRA Contig | Fraction of cell barcodes with at least one full-length TRA contig. |
| float | Cells With Productive TRA Contig | Fraction of cell barcodes with at least one full-length TRA contig that is productive. |
| float | Cells With Productive V-J Spanning Pair | Fraction of cell barcodes with at least one contig for each chain of the receptor pair that is productive. |