Long CDR3 sequences

[Januaryyiyue]

I am using the analyze command with MiXCR version 4.6. I got the following CDR3 alpha clone:
CCLKDTFLPDTMYWGSSKVFRNDACGSALTAQLFF
This seems to be an artefact. How can I remove such clones (e.g., clones longer than 20aas) from my analysis? Especially from the .clns file, because I am also using the .clns file for postanalysis.

Thank you so much.

[mizraelson]

Hi,
If you can export a list of clone IDs (excluding the IDs of the clones you want to filter out, for example, based on the length of the aaSeqCDR3) in a TSV file as a column of numbers, you can then run:

mixcr slice \
    --ids-file ids.tsv \
    input.clns \
    filtered.clns

filtered.clns will only contain the clones specified in the ids.tsv file.

[Januaryyiyue]

Thank you so much!