Missing AIRR TSV Fields After mixcr exportAirr on .clna Output from RNA-seq Preset

[BIGM0RPH]

Hello,

I ran into an issue while working with MiXCR’s rna-seq preset. After running the analysis and exporting the results in AIRR format, several columns in the resulting .tsv file were completely empty.

Commands used:

mixcr analyze rna-seq --species hsa example_1.fq example_2.fq output
mixcr exportAirr output.clna mixcr_output.airr.tsv

The pipeline completed without any errors, and the .clna file was successfully generated. However, when exporting the AIRR file, the following fields were all empty:

cdr1, cdr1_aa, cdr2, cdr2_aa, 
fwr1, fwr1_aa, fwr2, fwr2_aa, 
fwr3, fwr3_aa, fwr4, fwr4_aa, 
c_score, c_cigar, 
c_germline_start, c_sequence_start, 
c_germline_end, c_sequence_end, 
c_alignment_start, c_alignment_end

I tested this on both TCR and BCR RNA-seq datasets, and the issue persisted for both types. The output file is generated, but those fields are consistently blank. Based on this I have a few questions I'd like to ask:

• Is this expected behavior when using the rna-seq preset?
• Could this be related to the type or quality of the input data?
• Is there any configuration or additional step required to ensure these fields are populated?

Thank you so much for any help!

[mizraelson]

Hi,
What version of MiXCR are you using? For bulk RNA-seq it is common that there is not enough data to reconstruct the full length of the receptor so these columns will be empty for such clones. CDR3 sequence is the minimum requirement for a clone to be identified so this region will present for all clones.

[BIGM0RPH]

Thank you for the clarification.

I'm using MiXCR v4.7.0.

That makes sense — I was running this on bulk RNA-seq data, so it's helpful to know that incomplete coverage can lead to missing values in those AIRR fields. Good to know that CDR3 is the minimum required for clone identification and that it's expected behavior for other regions (like CDR1, CDR2, FWRs, etc.) to be missing in such cases.

Appreciate your quick response!