Cell Ranger7.1, printed on 03/04/2024
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:
|Estimated Number of Cells
|The number of barcodes estimated to correspond to GEMs containing cells. See VDJ Cell Calling Algorithm.
|Mean Read Pairs per Cell
|Number of input read pairs divided by the estimated number of cells.
|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).
|Number of Read Pairs
|Total number of read pairs that were assigned to this library in demultiplexing.
|Fraction of reads with barcodes that match the whitelist after barcode correction.
|Q30 Bases in Barcode
|Fraction of cell barcode bases with Q-score ≥ 30.
|Q30 Bases in RNA Read 1
|Fraction of read 1 bases with Q-score ≥ 30. (Likewise for read 2.)
|Q30 Bases in Sample Index
|Fraction of sample index bases with Q-score ≥ 30.
|Q30 Bases in UMI
|Fraction of UMI bases with Q-score ≥ 30.
|Reads Mapped to Any V(D)J Gene
|Fraction of reads that partially or wholly map to a V(D)J gene segment.
|Reads Mapped to TRA
|Fraction of reads that map partially or wholly to a TRA gene segment.
|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.
|Fraction Reads in Cells
|Number of reads with cell barcodes divided by the number of reads with valid barcodes.
|Median TRA UMIs per Cell
|Median number of UMIs assigned to a TRA contig per cell.
|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.
|Cells With TRA Contig
|Fraction of cell barcodes with at least one TRA contig annotated as a full or partial V(D)J gene.
|Cells With CDR3-annotated TRA Contig
|Fraction of cell barcodes with at least one TRA contig where a CDR3 was detected.
|Cells With V-J Spanning Contig
|Fraction of cell barcodes with at least one full-length contig.
|Cells With V-J Spanning TRA Contig
|Fraction of cell barcodes with at least one full-length TRA contig.
|Cells With Productive TRA Contig
|Fraction of cell barcodes with at least one full-length TRA contig that is productive.
|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.
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