human gdTRC support?

[dchutc]

Hi,

Possibly the same as to Dharamendra's question: Is it similarly straightforward to add support for human gamma delta TCRs?

Best regards, Don

[aqzas]

Hi, dchutc

Sorry for the late reply. To add support for human gamma delta TCRs (or some other custom genome ), user need to add some settings in reference.jl.
For example, to add support gamma chain CDR3 region, one should add an option in refg, follow the rule and syntax of other options, which should be like:

"hs" => Dict(
    "TRB"=>Dict(...),
    "TRA"=>Dict(...),
    "IGH"=>Dict(...),
    "TRG"=>Dict(
         "CDR3" => Dict(
                "vregion" => "",
                "jregion" => "",
                "cmotif" => "",
                "fmotif" => "",
                "coffset" => ,
                "foffset" => ,
                "innerC" => "place_holder",
                "innerF" => "place_holder",
            ),
    )
)

where

• vregion and jregion are the path of reference genome (nucleic acid sequence)
• cmotif and fmotif are the motif pattern in head and tail of gamma chain CDR3s.
• coffset and foffset are the offset of C104 and F114 in the patterns above.
• innerC and innerF are also the motif pattern in head and tail of gamma chain CDR3s, but innerC should begin with the 'C' and innerF' should end with 'F'. This option is used to rescue some CDR3s that don't contain complete motifs in cmotifandfmotif`. (optional, just fill "place_holder" is not needed).

Additionally, 'TRG' should be add to catt Line 16, like

    parser.add_argument("--chain", default="TRB", choices=['TRB', 'TRA', 'IGH', 'TRG'])

[dchutc]

Thanks!

[sciencepeak]

Hi, aqzas,

Could you please update the --chain parameters in the next version of CATT tool, so it can handle all TRA, TRB, TRD, TRG for human? That would be much more user-friendly than letting users to edit the source code.

Thanks.