Default parameters and differences between the built-in preset 'rnaseq-full-length' and 'rnaseq-cdr3'

[a-r-j-w]

Hi there,

I have two questions related to the built-in mixcr analyze rnaseq-full-length and mixcr analyze rnaseq-cdr3 presets, and hope that this is the correct forum to ask:

1. Where can I find the default parameters for each preset? In particular, I was hoping to see what the default parameter is for the --chains parameter of mixcr export. I would like to have TRA, TRD, TRB and TRG exported separately, but instead after running the mixcr analyze rnaseq-full-length preset, I only see TRAD, TRB and TRG. I am not sure how to interpret the output of TRAD. For eg, can I infer which alignments pertain to TRD vs TRA from the clones_TRAD.tsv file, or should I reanalyze the results by specifying that I would like TRA, TRD, TRB and TRG separately?

2. If I am only interested in analyzing TCR rearrangements, is it ok that I used the mixcr analyze rnaseq-full-length preset, or should I have used the mixcr analyze rnaseq-cdr3 preset?

Thanks in advance for your help.