How to extract TCR-β sequences from RNA-seq data more comprehensively?

[linqy-immune]

Hi, @mizraelson
Long time no see, best wishes for you in 2026.
There is a batch of RNA-seq data (mainly transcriptome) of interested disease, I am so sad that I can't find the TCR-seq data for that. But thanks to mixcr, such a powerful package, I find that I can attempt to extract TCR data from RNA-seq data by mixcr align --parameters rna-seq -OallowPartialAlignments=true data_R1.fastq.gz data_R2.fastq.gz alignments.vdjca.
But after running this code, it seems that something wrong happens, WARNING: unnecessary override -OallowPartialAlignments=true with the same value. And there are only 37 TCR-beta sequences in the final export file.

How could I obtain more TCR-beta sequences with high quality? I would appreciate it if you give me some instructions about this!!!
Looking forward to your reply.
Thanks and best regards,
Linqy

[mizraelson]

Hi,
-OallowPartialAlignments=true is laready included in the rna-seq preset so the override is unnecessary. Unfortunately a low yield for bulk RNA-seq data is expected and there is not much else we can do. Running the command bellow is the correct approach:

mixcr analyze rna-seq -s hsa data_R1.fastq.gz data_R2.fastq.gz output