issues with BD Rhapsody TCR data

[BDXH-FY24]

Hi,

I have issues to run coNGA with BD RHapsody TCR mouse data:

screenshot:

Looking forward to your reply

[sschattgen]

Hello. Thanks for your interest in conga. There are two issues I can see here.

First is that those particular alleles for TRAV15D-1/DV6 an TRAV13-2 seem new, and thus are not in the seq database for tcrdist. There's a check in play to drop any TCRs which genes are not within it. I've updated the database and added these in. Try it again using the latest commit to the master branch.

Second, you seem to be running ab and gd together. Conga is not setup for this and expects these will be run separately. I suspect the organism was set to 'mouse' when you tried. If that's the case then the Trdj will not be recognized since it assumes we should only be looking at the VJ genes relevant to abTCRs. Try splitting into ab and gd, then run using 'mouse' and 'mouse_gd' for organism, respectively.