B cell lineage tree

[Januaryyiyue]

Is it possible to do B cell lineage analysis but not use analyze? For my custom analysis I am running align, assemblePartial, extend and exportClones.

If so, which starting files from my custom analysis should I use to build the tree? Or is it better to somehow incorporate all these steps into analyze?

Thank you

[mizraelson]

What kind of data do you have? RNA-seq?

[Januaryyiyue]

Hi, Thank you for your prompt response. I am using the RNA-seq preset. The method I used is a targeted-sequencing technique (CapIG-seq) that captures the 3' of the V region, the CDR3 region and the 5' of the J region. Best

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________________________________ From: mizraelson ***@***.***> Sent: October 31, 2023 10:43 PM To: milaboratory/mixcr ***@***.***> Cc: Yi Yue Jiang ***@***.***>; Author ***@***.***> Subject: Re: [milaboratory/mixcr] B cell lineage tree (Discussion #1420) You don't often get email from ***@***.*** Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> What kind of data do you have? RNA-seq? — Reply to this email directly, view it on GitHub<#1420 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AUB7ZH3I7SIJ7WEGQJHZI4LYCGZOLAVCNFSM6AAAAAA6YQFWESVHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM3TINBRGQ2TE>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[mizraelson]

Since this protocol utilizes DNA (as indicated in the publication I have found, correct?), the appropriate command should be:

mixcr analyze exome-seq \
    --species hsa \
      input_R1.fastq.gz \
      input_R2.fastq.gz \
      result

This preset includes the steps align, assemblePartial, extend, assembleContigs, and exportClones. Please note that extend is automatically used for only TCR data. We can't apply it for BCR CDR3 extension due to potential hypermutations.

Utilizing this data for tree reconstruction will be quite challenging as it doesn't cover the full length of V and J genes comprehensively. Nevertheless, tree reconstruction necessitates equal coverage of all clones (i.e., the same gene segments must be covered). To filter clones based on this criteria, you can use the --assemble-contigs-by {FR3Begin:FR4End} parameter. Be sure to adjust the gene feature to match the coverage in your data.

Let me know if you need any further clarification.