exportAlignments -readIds parameter exports numeric index ‘0‘ instead of actual FASTQ read identifiers

[biomaticss]

Dear mixcr Team,
When using the mixcr exportAlignments -readIds commands, the readId column in the output TSV files contains only a numeric index (0, 1, 2...) instead of the original FASTQ read identifiers (e.g., VH30000833L1C001R0010000000/1 ) This prevents linking MiXCR analysis results back to the original sequences for downstream barcode-based pairing. I want get the original FASTQ read identifiers.
My command
mixcr exportAlignments -readIds -cloneId -vHit -jHit -aaFeature CDR3 sample.vdjca sample.tsv
Result
readId targetSequences ... cloneId ...
0 CTAGGTCG... ... -1 ...
My MIXCR version : v4.7.0
Is this the expected behaviour? Can I get the original FASTQ read identifiers?
Any comment from your side is very appreciated.
best,
Phoebe

[mizraelson]

Hi, yes, you would first need to use -OsaveOriginalReads=true with mixcr align command (-Malign.saveOriginalReads=true if you use mixcr analyze). Then when you run mixcr exportAlignments add -descrsR1 -descrsR2.