Hello all, I am new to the airrflow pipeline. I may have missed this information, but I have a question regarding the use of genome version for in the non-targeted bulk RNA-seq based TCR analysis using TRUST4. In the original TRUST4, there is a possibility to use hg19 or hg38 (or even make a custom one). But I am not sure, which version is being used? or are there parameters to set the path, etc? Thank you so much in advance!

Hi Jay, by default airrflow uses a pre-downloaded version of the imgt database. However, you could also build you own reference (e.g. using the trust4 command) and use this in airrflow by setting the

--reference_fasta

flag

Thank you Mark. yes, make sense then!