per-chain column options: These options define per-chain variables, which correspond to columns
that appear once for each chain in each clonotype, and have one entry for each exact subclonotype.
Please note that for medians of integers, we actually report the "rounded median", the result of
rounding the true median up to the nearest integer, so that e.g. 6.5 is rounded up to 7.
See also enclone help lvars and the inventory of all variables at
https://10xgenomics.github.io/enclone/pages/auto/inventory.html.
Per-column variables are specified using
CVARS=x1,...,xn
where each xi is one of:
┌─────────────────┬──────────────────────────────────────────────────────────────────────────────┐
│var │ bases at positions in chain that vary across the clonotype │
├─────────────────┼──────────────────────────────────────────────────────────────────────────────┤
│u │ ● VDJ UMI count for each exact subclonotype, median across cells │
│r │ ● VDJ read count for each exact subclonotype, median across cells │
├─────────────────┼──────────────────────────────────────────────────────────────────────────────┤
│edit │ a string that defines the edit of the reference V(D)J concatenation versus │
│ │ the contig, from the beginning of the CDR3 to the end of the J segment; │
│ │ this uses a coordinate system in which 0 is the first base of the J ref │
│ │ segment (or the first base of the D ref segment for IGH and TRB); for │
│ │ example D-4:4 denotes the deletion of the last 4 bases of the V segment, │
│ │ I0:2 denotes an insertion of 2 bases after the V │
│ │ and I0:2•S5 denotes that plus a substitution at position 5; in computing │
│ │ "edit", for IGH and TRB, we always test every possible D segment, │
│ │ regardless of whether one is annotated, and pick the best one; for this │
│ │ reason, "edit" may be slow │
│comp │ a measure of CDR3 complexity, which is the total number of S, D and I │
│ │ symbols in "edit" as defined above │
│cigar │ the CIGAR string that defines the edit of the V..J contig sequence versus │
│ │ the universal reference V(D)J concatenation │
├─────────────────┼──────────────────────────────────────────────────────────────────────────────┤
│cdr*_aa │ the CDR*_AA sequence, or "unknown" if not computed │
│cdr*_aa_L_R_ext │ the CDR*_AA sequence, with L amino acids added on the left and R amino acids│
│ │ added on the right; either may be negative, denoting trimming instead │
│ │ of extension │
│cdr*_aa_north │ the CDR*_AA sequence for BCR defined by North B et al. (2011), A new │
│ │ clustering of antibody CDR loop conformations, J Mol Biol 406, 228-256. │
│ │ cdr1_aa_north = cdr1_aa_3_3_ext for heavy chains │
│ │ cdr1_aa_north = cdr1_aa for light chains │
│ │ cdr2_aa_north = cdr2_aa_2_3_ext for heavy chains │
│ │ cdr2_aa_north = cdr2_aa_1_0_ext for light chains │
│ │ cdr3_aa_north = cdr3_aa_-1_-1_ext │
│cdr*_aa_ref │ cdr*_aa, for the universal reference sequence (but not for cdr3) │
│cdr*_len │ number of amino acids in the CDR* sequence, or "unknown" if not computed │
│cdr*_dna │ the CDR*_DNA sequence, or "unknown" if not computed │
│cdr*_dna_ref │ same, for the universal reference sequence (but not for cdr3) │
├─────────────────┼──────────────────────────────────────────────────────────────────────────────┤
│cdr3_aa_conx │ consensus for CDR3 across the clonotype, showing X for each variant residue │
│cdr3_aa_conp │ consensus for CDR3 across the clonotype, showing a property symbol whenever │
│ │ two different amino acids are observed, per the following table: │
│ │ -------------------------------------------------------------------- │
│ │ asparagine or aspartic acid B DN │
│ │ glutamine or glutamic acid Z EQ │
│ │ leucine or isoleucine J IL │
│ │ negatively charged - DE │
│ │ positively charged + KRH │
│ │ aliphatic (non-aromatic) Ψ VILM │
│ │ small π PGAS │
│ │ aromatic Ω FWYH │
│ │ hydrophobic Φ VILFWYM │
│ │ hydrophilic ζ STHNQEDKR │
│ │ any X ADEFGHIKLMNPQRSTVWY │
│ │ -------------------------------------------------------------------- │
│ │ The table is searched top to bottom until a matching class is found. │
│ │ In the special case where every amino acid is shown as a gap (-), │
│ │ a "g" is printed. │
├─────────────────┼──────────────────────────────────────────────────────────────────────────────┤
│fwr*_aa │ the FWR*_AA sequence, or "unknown" if not computed │
│fwr*_aa_ref │ same, for the universal reference sequence │
│fwr*_len │ number of amino acids in the FWR* sequence, or "unknown" if not computed │
│fwr*_dna │ the FWR*_DNA sequence, or "unknown" if not computed │
│fwr*_dna_ref │ same, for the universal reference sequences │
│ │ For all of these, * is 1 or 2 or 3 (or 4, for the fwr variables). │
│ │ For CDR1 and CDR2, please see enclone help amino and the page on │
│ │ bit.ly/enclone on V(D)J features. │
├─────────────────┼──────────────────────────────────────────────────────────────────────────────┤
│v_start │ start of V segment on full DNA sequence │
│d_start │ start of D segment on full DNA sequence (or null) │
│cdr3_start │ base position start of CDR3 sequence on full contig │
│d_frame │ reading frame of D segment, either 0 or 1 or 2 (or null) │
├─────────────────┼──────────────────────────────────────────────────────────────────────────────┤
│aa% │ amino acid percent identity with donor reference, outside junction region │
│dna% │ nucleotide percent identity with donor reference, outside junction region │
├─────────────────┼──────────────────────────────────────────────────────────────────────────────┤
│v_name_orig │ name of V region originally assigned (per cell); │
│ │ values below are clonotype consensuses │
│utr_name │ name of 5'-UTR region │
│v_name │ name of V region │
│d_name │ name of D region (or null) │
│j_name │ name of J region │
│const │ name of constant region │
├─────────────────┼──────────────────────────────────────────────────────────────────────────────┤
│utr_id │ id of 5'-UTR region │
│v_id │ id of V region │
│d_id │ id of D region (or null) │
│j_id │ id of J region │
│const_id │ id of constant region (or null, if not known) │
│ │ (these are the numbers after ">" in the VDJ reference file) │
├─────────────────┼──────────────────────────────────────────────────────────────────────────────┤
│allele │ numerical identifier of the computed donor reference allele │
│ │ for this exact subclonotype │
│allele_d │ variant bases in the allele for this exact subclonotype, │
│ │ and a list of all the possibilities for this │
├─────────────────┼──────────────────────────────────────────────────────────────────────────────┤
│d1_name │ name of optimal D gene, or none │
│d2_name │ name of second best D gene, or none │
│d1_score │ score for optimal D gene │
│d2_score │ score for second best D gene │
│d_delta │ score difference between first and second best D gene │
│d_Δ │ same │
│ │ These are recomputed from scratch and ignore the given assignment. │
│ │ Note that in many cases D gene assignments are essentially random, as │
│ │ it is often not possible to know the true D gene assignment. │
│ │ If the value is "null" it means that having no D gene at all scores better │
├─────────────────┼──────────────────────────────────────────────────────────────────────────────┤
│vjlen │ number of bases from the start of the V region to the end of the J region │
│ │ Please note that D gene assignments are frequently "random" -- it is not │
│ │ possible to know the actual D gene that was assigned. │
│clen │ length of observed constant region (usually truncated at primer start) │
│ulen │ length of observed 5'-UTR sequence; │
│ │ note however that what report is just the start of the V segment │
│ │ on the contig, and thus the length may include junk before the UTR │
│cdiff │ differences with universal reference constant region, shown in the │
│ │ abbreviated form e.g. 22T (ref changed to T at base 22) or 22T+10 │
│ │ (same but contig has 10 additional bases beyond end of ref C region │
│ │ At most five differences are shown, and if there are more, ... is appended. │
│udiff │ like cdiff, but for the 5'-UTR │
├─────────────────┼──────────────────────────────────────────────────────────────────────────────┤
│q<n>_ │ comma-separated list of the quality │
│ │ scores at zero-based position n, numbered starting at the │
│ │ beginning of the V segment, for each cell in the exact subclonotype │
├─────────────────┼──────────────────────────────────────────────────────────────────────────────┤
│notes │ optional note if there is an insertion or the end of J does not exactly abut│
│ │ the beginning of C; elided if empty; also single base overlaps between │
│ │ J and C are not shown unless you use the special option JC1; we do this │
│ │ because with some VDJ references, one nearly always has such an overlap │
├─────────────────┼──────────────────────────────────────────────────────────────────────────────┤
│ndiff<n>vj │ number of base differences within V..J between this exact subclonotype and │
│ │ exact subclonotype n │
│d_univ │ distance from universal reference, more specifically, │
│ │ number of base differences within V..J between this exact │
│ │ clonotype and universal reference, exclusive of indels, the last 15 │
│ │ bases of the V and the first 15 bases of the J │
│d_donor │ distance from donor reference, │
│ │ as above but computed using donor reference │
└─────────────────┴──────────────────────────────────────────────────────────────────────────────┘
● These variables have some alternate versions, as shown in the table below.
┌──────────┬───────────────────────────────┬──────────┬──────────────┬─────────────┬────────────┐
│variable │ semantics │ visual │ visual │ parseable │ parseable │
│ │ │ │ (one cell) │ │ (one cell)│
├──────────┼───────────────────────────────┼──────────┼──────────────┼─────────────┼────────────┤
│x │ median over cells │ yes │ this cell │ yes │ yes │
│x_mean │ mean over cells │ yes │ null │ yes │ yes │
│x_μ │ (same as above) │ yes │ null │ yes │ yes │
│x_sum │ sum over cells │ yes │ null │ yes │ yes │
│x_Σ │ (same as above) │ yes │ null │ yes │ yes │
│x_min │ min over cells │ yes │ null │ yes │ yes │
│x_max │ max over cells │ yes │ null │ yes │ yes │
│x_% │ % of total GEX (genes only) │ yes │ this cell │ yes │ yes │
│x_cell │ this cell │ no │ no │ no │ this cell │
└──────────┴───────────────────────────────┴──────────┴──────────────┴─────────────┴────────────┘
Some explanation is required. If you use enclone without certain options, you get the "visual"
column.
• Add the option PER_CELL (see enclone help display) and then you get visual output with extra
lines for each cell within an exact subclonotype, and each of those extra lines is described by
the "visual (one cell)" column.
• If you generate parseable output (see enclone help parseable), then you get the "parseable"
column for that output, unless you specify PCELL, and then you get the last column.
• For the forms with μ and Σ, the Greek letters are only used in column headings for visual output
(to save space), and optionally, in names of fields on the command line.
▶ If you try out these features, you'll see exactly what happens! ◀
At least one variable must be listed. The default is u,const,notes. CVARSP: same as CVARS but
appends.