Hi, I still have a user question. Just want to confirm when airrflow pipeline does the repertoire analysis, does it use only TCRb information, right? Or both TCRb and TCRa? Because, Cellranger VDJ generates TCRb and TCRa, but I only found TCRb calls in airrflow "repertoires" folder ??

@Jin LU which species are you analyzing: human or mouse?

I am analyzing mouse. By looking at shazam document for single cells, it seems to me that the program only uses TCRb information. Thanks

If you would like to still have the TCRalpha information on the output repertoire files and define clones according to TCRb and split them also according to TCRa, you can resume the pipeline providing the additional configuration

-c custom.config

as a parameter, containing:

process{
   withName: CHANGEO_MAKEDB{
     ext.args = '--regions default --format airr --extended --partial'
  }
}

My check is correct. The current pipeline of airrflow only considers TCRb as clones. The next version would include both TCRb and TCRa as default. BTW, I found current version uses cellranger 7.1. Now many people use cellranger >8.0. Hope the team can upgrade it. Thanks a lot, a very useful tool!