Including Leaders in Custom Reference

[pursellta]

Hello!
I am trying to generate a custom reference for a non-model organism from my genome annotations. I wanted to include the leader sequences (i.e. Vtranscript) to improve the V-gene calling as my libraries are 5'RACE, but when I run the following code:
mixcr buildLibrary --debug --v-genes-from-fasta IGHVwLeaders.fasta --v-gene-feature VTranscript --j-genes-from-fasta IGHJ.fasta --d-genes-from-fasta IGHD.fasta --c-genes-from-fasta IGHC.fasta --chain IGH --taxon-id 29078 --species epfu IGH-V2.json.gz
It fails to extract the VTranscript. I have successfully generated and used a library using the VRegion as suggested in the documentation. I am using v4.6.0.
Thanks for your help!

[pursellta]

UPDATE: It still doesn't work when I change the feature to VTranscriptWithout5UTR which more accurately describes my input sequence. That said, I was able to get it to work by altering the input to be from L1Begin to VEnd and using the feature VGene but it sometimes falsely puts some of the L1 as V5UTR.

[mizraelson]

Hi,
Can you please forward this request to support@milaboratories.com