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glossary of terms used by enclone

│V..J                │  the full sequence of a V(D)J transcript, from the beginning of the V       │
│                    │  segment to the end of the J segment; this sequence begins with a stop codon│
│                    │  and ends with a partial codon (its first base)                             │
│CDR3                │  The terms CDR3 and junction are commonly mistaken and often                │
│                    │  used interchangeably.  In enclone's nomenclature, "CDR3"                   │
│                    │  actually refers to the junction (the CDR3 loop plus the                    │
│                    │  canonical C and W/F at the N and C termini respectively).                  │
│clonotype           │  all the cells descended from a single fully rearranged T or B cell         │
│                    │  (approximated computationally)                                             │
│exact subclonotype  │  all cells having identical transcripts                                    │
│                    │  (every clonotype is a union of exact subclonotypes)                        │
│clone               │  a cell in a clonotype, or in an exact subclonotype                         │
│onesie              │  a clonotype or exact subclonotype having exactly one chain                 │
│twosie              │  a clonotype or exact subclonotype having exactly two chains                │
│threesie            │  a clonotype or exact subclonotype having exactly three chains;             │
│                    │  these frequently represent true biological events, arising from expression │
│                    │  of both alleles                                                            │
│foursie             │  a clonotype or exact subclonotype having exactly four chains;              │
│                    │  these very rarely represent true biological events                         │
│moresie             │  a clonotype having more than four chains;                                  │
│                    │  these sad clonotypes do not represent true biological events               │
│donor               │  an individual from whom datasets of an origin are obtained                 │
│origin              │  a tube of cells from a donor, from a particular tissue at a                │
│                    │  particular point in time, and possibly enriched for particular cells       │
│cell group          │  an aliquot from an origin, presumed to be a random draw                    │
│dataset             │  all sequencing data obtained from a particular library type                │
│                    │  (e.g. TCR or BCR or GEX or FB), from one cell group, processed by running  │
│                    │  through the Cell Ranger pipeline                                           │

 The exact requirements for being in the same exact subclonotype are that cells:
• have the same number of productive contigs identified
• that these have identical bases within V..J
• that they are assigned the same constant region reference sequences
• and that the difference between the V stop and the C start is the same
  (noting that this difference is nearly always zero).
Note that we allow mutations within the 5'-UTR and constant regions.


• When we refer to "V segments", we always include the leader segment.
• Zero or one?  We number exact subclonotypes as 1, 2, ... and likewise with
chains within a clonotype, however DNA and amino-acid positions are numbered starting at zero.