how to generate .clna file from analyze takara-human-rna-tcr-umi-smartseq preset command

[PaulDanPhillips]

I am trying to generate the read files of just those that aligned using the mixcr exportReadsForClones command. Unfortunately, this will not work with the *.clns files generated and I do not see how to force generating the *.clna files from the analyze takara-human-rna-tcr-umi-smartseq preset command. Is there a way to convert from *.clns to *.clna or to generate *.clna from the analyze command that I am not seeing?

[mizraelson]

To obtain the .clna file, you should add these two parameters during the analysis with mixcr analyze:

-Malign.parameters.saveOriginalReads=true
-Massemble.clnaOutput=true

Afterward, you can run exportReadsForClones using the .clna file.