How to select best V/J genes?

[louis-jliu]

Hi,

My TRB sample columns are like below:

'barcode', 'umis', 'cdr3_nt','cdr3', 'v_gene','j_gene'

I ranked them based on umi values and added a column of "rank", when I run ALICE with it, error as below:

     Error in FUN(X[[i]], ...) : object 'bestVGene' not found 

I noticed that in the demo dataset of S1:

unique(S1d0$bestJGene) [1] "TRBJ2-7" unique(S1d0$bestVGene) [1] "TRBV9"

Do I need to do a selection to find best V/J genes? Or how do i get the correct formatted input for ALICE?

Thanks in advance.