custom build databases

[bhartimittal2976]

Hello, I am working on different animal species eg cow, pig, rabbit etc. I would like to use their reference databases. I would like to get training on custom databases. How to get gene feature file for the respective species. I have the fasta files for each regions, Can I know how to get gene feature files. Please contact me at- bharti.mittal@pirbright.ac.uk

Looking forward to hearing,
Regards,
Bharti

[mizraelson]

Hi,

We have a dedicated command for creating a custom reference library. You can read the instructions here.

Briefly, to create a custom reference library, run the command below:

mixcr buildLibrary --debug \
  --v-genes-from-fasta v-genes.IGH.fasta \
  --v-gene-feature VRegion \
  --j-genes-from-fasta j-genes.IGH.fasta \
  --d-genes-from-fasta d-genes.IGH.fasta \ # optional
  --c-genes-from-fasta c-genes.IGH.fasta \ # optional
  --chain IGH \
  --taxon-id 9913 \
  --species cow \
  cow-IGH.json.gz

In this command:

• FASTQ files contain genes in regular FASTA format. For instance:

>IGHV12-348
GATGCTGGAGTTATCCAGTCACCCCGCCATGAGGTGACAGAGATGGG...

• --v-gene-feature defines which part of the V gene is provided in the FASTA file. Common values include:
  • VTranscript if your sequence contains the 5'UTR, Leader sequences, and the actual gene sequence from FR1.
  • VRegion if your FASTA files contain V gene sequences starting from FR1.

Simply put, VTranscript equates to V5UTR+L1+L2+VRegion.

If you're working with multiple chains (e.g., IGH, IGK, IGL), each chain should be processed separately. You can then merge them together using the command below:

mixcr mergeLibrary \
    cow-IGH.json.gz \
    cow-IGK.json.gz \
    cow-IGL.json.gz \
    cow.json.gz 

Subsequently, you can run MiXCR with your custom library using a command similar to the one below. Ensure you select the appropriate command based on your library preparation protocol. Also, make sure your library file (e.g., cow.json.gz) is located either in the same directory from which you're running MiXCR or in one of the directories indicated in the mixcr -v output.

mixcr analyze generic-amplicon \
    --library cow \
    --species cow \
    --rna \
    --rigid-left-alignment-boundary \
    --floating-right-alignment-boundary C \
    input_R1.fastq.gz \
    input_R2.fastq.gz \
    output

I hope this clarifies the process for you. Let me know if you need further assistance.

Sincerely,
Mark

[bhartimittal2976]

could you share the format of --v-gene-feature VRegion file format

[mizraelson]

--v-gene-feature VRegion is not a file but a parameter that defines the feature you have in your fasta file. In this case the sequences should cover everything from FR1 to the end of the V gene

[bhartimittal2976]

Thank you. Bharti

…

On Sat, Sep 9, 2023 at 7:05 PM mizraelson ***@***.***> wrote: Hi, We have a dedicated command for creating a custom reference library. You can read the instructions here <https://mixcr.com/mixcr/guides/create-custom-library/#de-novo-libraries>. Briefly, to create a custom reference library, run the command below: mixcr buildLibrary --debug \ --v-genes-from-fasta v-genes.IGH.fasta \ --v-gene-feature VRegion \ --j-genes-from-fasta j-genes.IGH.fasta \ --d-genes-from-fasta d-genes.IGH.fasta \ # optional --c-genes-from-fasta c-genes.IGH.fasta \ # optional --chain IGH \ --taxon-id 9913 \ --species cow \ cow-IGH.json.gz In this command: - FASTQ files contain genes in regular FASTA format. For instance: >IGHV12-348 GATGCTGGAGTTATCCAGTCACCCCGCCATGAGGTGACAGAGATGGG... - --v-gene-feature defines which part of the V gene is provided in the FASTA file. Common values include: - VTranscript if your sequence contains the 5'UTR, Leader sequences, and the actual gene sequence from FR1. - VRegion if your FASTA files contain V gene sequences starting from FR1. Simply put, VTranscript equates to V5UTR+L1+L2+VRegion. If you're working with multiple chains (e.g., IGH, IGK, IGL), each chain should be processed separately. You can then merge them together using the command below: mixcr mergeLibrary \ cow-IGH.json.gz \ cow-IGK.json.gz \ cow-IGL.json.gz \ cow.json.gz Subsequently, you can run MiXCR with your custom library using a command similar to the one below. Ensure you select the appropriate command based on your library preparation protocol. Also, make sure your library file (e.g., cow.json.gz) is located either in the same directory from which you're running MiXCR or in one of the directories indicated in the mixcr -v output. mixcr analyze generic-amplicon \ --library cow \ --species cow \ --rna \ --rigid-left-alignment-boundary \ --floating-right-alignment-boundary C \ input_R1.fastq.gz \ input_R2.fastq.gz \ output I hope this clarifies the process for you. Let me know if you need further assistance. Sincerely, Mark — Reply to this email directly, view it on GitHub <#1340 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AMYH6LO4NXKHUGKVK4QXZLTXZRWDHANCNFSM6AAAAAA4QFNEOA> . You are receiving this because you authored the thread.Message ID: ***@***.***>