10x Genomics Support/Cell Ranger 7.2/Analysis/

Metrics Output from the Cell Ranger vdj Pipeline

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:

  • In some cases there is a metric for each chain type. Only one is shown.
  • Cells refers to T or B cells.
  • References to quality scores exclude very low quality/no-call (Q ≤ 2) bases.
TypeNameDescription
intEstimated Number of CellsThe number of barcodes estimated to correspond to GEMs containing cells. See VDJ Cell Calling Algorithm.
intMean Read Pairs per CellNumber of input read pairs divided by the estimated number of cells.
intNumber of Cells With Productive V-J Spanning PairNumber 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).
intNumber of Read PairsTotal number of read pairs that were assigned to this library in demultiplexing.
floatValid BarcodesFraction of reads with barcodes that match the whitelist after barcode correction.
floatQ30 Bases in BarcodeFraction of cell barcode bases with Q-score greater than or equal to 30.
floatQ30 Bases in RNA Read 1Fraction of read 1 bases with Q-score greater than or equal to 30. (Likewise for read 2.)
floatQ30 Bases in Sample IndexFraction of sample index bases with Q-score greater than or equal to 30.
floatQ30 Bases in UMIFraction of UMI bases with Q-score ≥ 30.
floatReads Mapped to Any V(D)J GeneFraction of reads that partially or wholly map to a V(D)J gene segment.
floatReads Mapped to TRAFraction of reads that map partially or wholly to a TRA gene segment.
intMean Used Read Pairs per CellMean 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.
floatFraction Reads in CellsNumber of reads with cell barcodes divided by the number of reads with valid barcodes.
floatMedian TRA UMIs per CellMedian number of UMIs assigned to a TRA contig per cell.
floatPaired Clonotype DiversityEffective 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.
floatCells With TRA ContigFraction of cell barcodes with at least one TRA contig annotated as a full or partial V(D)J gene.
floatCells With CDR3-annotated TRA ContigFraction of cell barcodes with at least one TRA contig where a CDR3 was detected.
floatCells With V-J Spanning ContigFraction of cell barcodes with at least one full-length contig.
floatCells With V-J Spanning TRA ContigFraction of cell barcodes with at least one full-length TRA contig.
floatCells With Productive TRA ContigFraction of cell barcodes with at least one full-length TRA contig that is productive.
floatCells With Productive V-J Spanning PairFraction of cell barcodes with at least one contig for each chain of the receptor pair that is productive.