Numbering scheme for partis?

[Lmar Babrak]

Hi, 

What numbering scheme (ie IMGT, Kabat, Clothia) do you use to dilineate framework and cdr3 regions? Sorry if you've already answered but I haven't been able to find it.

Thanks

Lmar

[Duncan Ralph]

Hi,

We use IMGT numbering, with the caveats: 1) positions in partis output files all use 0-based indexing and 2) the partis key "cdr3_length" includes both conserved codons, whereas in the imgt terminology this should really be called "junction" length (sorry... I've looked at swapping these but it'd just be too error-prone).

And thanks for pointing out the ambiguity, I'm making a note to add to the manual.

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