Why would special letters happen in the results?

[linqy-immune]

Hi, @mizraelson
Long time no see. How are you recently?
I am very sorry to be here again cause I find that there are many special letters("_","*") in the mixcr output, which may pose bad influence on my post-analysis.

The code I run is mixcr analyze generic-amplicon --assemble-clonotypes-by CDR3 --species hsa --dna --floating-left-alignment-boundary --floating-right-alignment-boundary C, the data was SRR30320269.
Could you please give me some tips?

Looking forward to your reply!!!
Thanks a lot!
Linqy

[mizraelson]

Hi @linqy-immune, always happy to hear from you! So the special letters come from non functional clones:
_ - frame shift
* - stop codon

You can either filter them out in postanalysis or use the --export-productive-clones-only parameter to filter them out by MiXCR.

[linqy-immune]

Got it!
Thank you sooo much for your quick reply!