VDJ Metrics

File: [sample_name]_VDJ_metrics.csv

Metrics specific to TCR and BCR data, also broken down by chain and by cell type (experimental).

This file is only output when the experiment included an appropriate TCR/BCR assay, and the VDJ_Version option is selected.

Overall VDJ Metrics

Metric	Definition	Major contributing factors
Reads_Cellular_Aligned_to_VDJ	Number of reads with a valid cell label and UMI that aligned to a VDJ gene segment per chain category.	Sequencing quality Library quality
Reads_Contig_Assembled	Number of cellular VDJ aligned reads that were assembled into a contig.	Cell viability Library quality
Reads_VDJ _Annotated	Number of reads in contigs passing e-value quality filter.	Cell viability Library quality
Reads_Putative	Number of Reads_VDJ_Annotated that came from a putative cell.	Cartridge workflow performance
Reads_Corrected	Number of putative VDJ reads that are from dominant contigs and remain after distribution-based error correction.	Cell viability Library quality
Pct_Reads_Corrected	Percent reads of the above metric relative to Reads_ Contig_Assembled.	Cell viability Library quality
Mean_Reads_Corrected_per_Putative_Cell	Average corrected reads per putative cell.	Cell viability Library quality
Molecules_VDJ_Annotated	Number of molecules represented by reads in Reads_VDJ_Annotated metric.	Cell viability Library quality
Molecules_Corrected	Number of molecules represented by reads in Reads_Corrected metric.	Cell viability Library quality
Mean_Molecules_Corrected_per_Putative_Cell	Average number of molecules per putative cell (Molecules_Corrected_Putative / num putative cells).	Cell viability Library quality
Dominant_Contigs_Mean_Nucleotide_Length	Average protein-coding nucleotide length for all dominant contigs.	Library quality
Dominant_Contigs_Pct_Full_Length	Percent of dominant contigs from putative cells that are VDJ full length contigs.	Library quality
Dominant_Contigs_Pct_With_CDR3	Percent of dominant contigs from putative cells with CDR3.	Library quality
Chain_Category	Category for chains such as BCR and TCR.	VDJ recombination

Chain type metrics

Chain type metrics are identical to overall metrics except that they are split by VDJ chain type, such as TCR Alpha and BCR Kappa.

Cell type metrics

Metric	Definition	Major contributing factors
Cell_Type_Experimental	Inferred cell type. Cell type is inferred, either from the mRNA targeted panel expression data or from relative counts of BCR vs TCR	Sample type mRNA panel
Number_cells	Number of cells classified as this cell type.	Sample type
BCR_Paired_Chains_Pct_Any	Percent of cells of each type that had both a BCR heavy chain and BCR light chain (Kappa or Lambda).	Cell viability Library quality
TCR_Paired_Chains_Pct_Any	Percent of cells of each type that had either TCR Alpha and TCR Beta, or TCR Gamma and TCR Delta.	Cell viability Library quality
BCR_Paired_Chains_Pct_Full	Percent of cells of each type that had full-length contigs for both BCR heavy chain and BCR light chain (Kappa or Lambda).	Cell viability Library quality
TCR_Paired_Chains_Pct_Full	Percent of cells of each type that had full-length contigs for either TCR Alpha and TCR Beta, or TCR Gamma and TCR Delta.	Cell viability Library quality
[chain_type]_Pct_Cells_Positive	Percent of cells of each cell type that had at least one valid corrected contig of the listed chain type.	Cell viability Library quality
[chain_type]_Pct_Cells_Full_Length	Percentage of cells from each cell type which had a full length contig with the listed chain type.	Cell viability Library quality
[chain_type]_Mean_Molecules_per_Cell	Mean number of corrected molecules of the listed chain type in each cell type.	Cell viability Library quality

High Quality Filtered Cell Metrics

High quality filtered cell metrics are identical to cell type metrics, but only for the subset of cells that were designated high-quality B or T cells, as described in the TCR/BCR analysis steps.

VDJ DBEC Graphs

File: [sample_name]_VDJ_DBEC_images.tar.gz

A tar.gz file archive containing a PNG image file for each chain type that underwent VDJ DBEC correction. The PNG file depicts a histogram of the "Chain Read Counts per Cell Label" on a Log10 scale. A vertical dotted red line indicates the location of the DBEC threshold that was applied. If a chain type did not have sufficient read depth to undergo DBEC correction, an image will not be generated for that type.