VDJ Per Cell

File: [sample_name]_VDJ_perCell.csv

Putative cells only, cell order is the same as gene expression data table (RSEC/DBEC_MolsPerCell_MEX.zip). Only dominant contigs, all error correction applied.

Data columns: Read and molecule counts, VDJ gene segments, CDR3 sequence, pairing, and cell type.

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

Metric	Definition	Major contributing factors
Cell_Index	Unique cell ID for the cell represented by this row. Cell index will match between VDJ data and gene/AbSeq expression data tables.	Sequencing quality Library quality
Total_VDJ_Read_Count	Total number of error-corrected VDJ reads for all chains in the cell.	Cell viability Library quality
Total_VDJ_Molecule_Count	Total number of error-corrected VDJ molecules for all chains in the cell.	Cell viability Library quality
[chain_type]_V_gene_Dominant	Dominant V gene segment identified for this chain type in the cell.	VDJ recombination
[chain_type]_D_gene_Dominant	Dominant D gene segment identified for this chain type in the cell.	VDJ recombination
[chain_type]_J_gene_Dominant	Dominant J gene segment identified for this chain type in the cell.	VDJ recombination
[chain_type]_C_gene_Dominant	Dominant C gene segment identified for this chain type in the cell.	VDJ recombination
[chain_type]_CDR3_Nucleotide_Dominant	Nucleotide sequence of the dominant clone for this chain type in the cell.	VDJ recombination
[chain_type]_CDR3_Translation_Dominant	Amino acid sequence of the dominant clone for this chain type in the cell.	VDJ recombination
[chain_type]_Read_Count	Number of error-corrected reads for this chain type in the cell.	Cell viability Library quality
[chain_type]_Molecule_Count	Number of unique error-corrected molecules (UMI)for this chain type in the cell.	Cell viability Library quality
BCR_Paired_Chains	True/False — this cell contains at least one error-corrected molecule of each BCR heavy and light (Kappa or Lambda).	Cell viability Library quality
TCR_Paired_Chains	True/False — this cell contains at least one error-corrected molecule of each TCR Alpha and TCR Beta, or TCR Gamma and TCR Delta.	Cell viability Library quality
Cell_Type_Experimental	Inferred cell type of this cell index. Cell type is inferred, either from the mRNA targeted panel expression data or from relative counts of BCR vs TCR.	Sample type mRNA panel
High_Quality_Cell	True/False - this cell was designated as high quality, having a B or T type, a productive contig, and sufficient VDJ molecules	Sample quality Library quality

VDJ Per Cell Uncorrected

File: [sample_name]_VDJ_perCell_uncorrected.csv

All cell IDs – putative and non-putative.

Only dominant contigs, no error correction, no chain family consolidation.

Data columns: Read and molecule counts, VDJ gene segments, CDR3 sequence, pairing, and cell type.

Shared column definitions are identical to the VDJ_perCell.csv file. Here are listed the columns unique to this file.

Metric	Definition	Major contributing factors
Putative_ Cell	True/False — this cell index was selected as a putative cell based on the mRNA Panel.	Cell viability mRNA Panel