Number of cells with V-J spanning productive paired TRA and TRB: Fraction of cell-associated barcodes with one productive contig for each chain of the receptor pair. A productive contig satisfies the following conditions: the contig annotations span the 5' end of the V region to the 3' end of the J region of the chain, a start codon was found in the expected part of the V sequence, an in-frame CDR3 amino acid motif was found, and no stop codons were found in the aligned V-J region.
Cells With TRA Contig: Fraction of cell-associated barcodes with at least one TRA contig annotated as a full or partial V(D)J gene.
Cells With V-J spanning TRA Contig: Fraction of cell-associated barcodes with at least one contig spanning the 5' end of the V region to the 3' end of the J region for TRA.
Cells With productive TRA Contig: Fraction of cell-associated barcodes with productive TRA chain. A productive contig satisfies the following conditions: the contig annotations span the 5' end of the V region to the 3' end of the J region of the chain, a start codon was found in the expected part of the V sequence, an in-frame CDR3 amino acid motif was found, and no stop codons were found in the aligned V-J region.
Cells With TRB Contig: Fraction of cell-associated barcodes with at least one TRB contig annotated as a full or partial V(D)J gene.
Cells With V-J spanning TRB Contig: Fraction of cell-associated barcodes with at least one contig spanning the 5' end of the V region to the 3' end of the J region for TRB.
Cells With productive TRB Contig: Fraction of cell-associated barcodes with productive TRB chain. A productive contig satisfies the following conditions: the contig annotations span the 5' end of the V region to the 3' end of the J region of the chain, a start codon was found in the expected part of the V sequence, an in-frame CDR3 amino acid motif was found, and no stop codons were found in the aligned V-J region.