Can analyze shotgun use input file name expansion?

[DawnChou]

Hi,
I'm trying to use MiXCR for antigen receptor calling of TCRbeta, and I have two Read 2 files from different lanes. GSM5416366_patient_16_S1_R2_L001.fastq.gz and GSM5416366_patient_16_S1_R2_L002.fastq.gz
I found https://mixcr.com/mixcr/reference/ref-input-file-name-expansion/ says {{n}} can match any number, so I input
mixcr analyze shotgun /public/yipingzou2/spatialTCR/GSM5416366_patient_16_S1_R2_L{{n}}.fastq.gz mixcr_output_3/clones --species hsa --starting-material rna --align "-OsaveOriginalReads=true" --assemble "--write-alignments"

However, it returns
ERROR: input file "/public/yipingzou2/spatialTCR/GSM5416366_patient_16_S1_R2_L{{n}}.fastq.gz" does not exist.

I checked the prefix again and again, but I did not find anything wrong. I'm new to mixcr and am unsure if I can use the input file name expansion here. Thanks for your help.

[mizraelson]

Hi,
What MiXCR version do you use?

[DawnChou]

Hi, What MiXCR version do you use?

I am using mixcr 3.0.13

[mizraelson]

The Lane merging feature is only available starting v4. I recommend updating to the latest version.

[DawnChou]

The Lane merging feature is only available starting v4. I recommend updating to the latest version.

OK. Thank you!

[mizraelson]

Also please note that some commands have changed and mixcr analyze shotgun has been deprecated.

For RNA-seq data the correct command will be:

mixcr analyze rnaseq-full-length \
    --species hsa 
    /public/yipingzou2/spatialTCR/GSM5416366_patient_16_S1_R2_L{{n}}.fastq.gz \
    mixcr_output_3/clones

You can read more here:
https://mixcr.com/mixcr/reference/overview-built-in-presets/#rna-seq-data