Exp_clones in bulk data

[licmn]

❓ Questions and Help

We have a set of listed tutorials available on the website.

I was wondering how the number of clones is calculated for bulk data. My understanding is that for bulk data you loose the ability to resolve the pairing of TCRα and TCRβ chains, and therefore clone numbers.

[vadimnazarov]

Dear Dr. Luisa Morales-Nebreda,

Thank you for using immunarch! The number of clones is calculated via the number of reads aligned to a specific clonotype or the number of Unique Molecular Identifiers assigned to immune cells. It is possible to reconstruct alpha/beta pairing for overabundant clonotypes using bulk sequencing data. Still, yes, it's much better to use single-cell sequencing if your goal is to analyze paired data.

Would you mind sharing more details on the project you have in mind? We worked with Northwestern on immunotherapy in the past, and we are in the space of combining single-cell transcriptomics and immunomics, so I believe we could help. Please let me know if a call would be more convenient for you rather than a response here.

Best, Vadim

[licmn]

Hi Vadim,

Thanks so much for your response! Sure, happy to share what are thoughts are for this project. I’m free:

• Thursday 2/3 from 10-12 and 1-3 CST
• Friday 2/4 10-12 and 1-3 CST

Can find other dates and time if these don’t work for you.

Best, Luisa

From: Vadim I. Nazarov @.> Sent: Friday, January 28, 2022 2:14 PM To: immunomind/immunarch @.> Cc: Luisa Morales-Nebreda @.>; Author @.> Subject: Re: [immunomind/immunarch] Exp_clones in bulk data (Issue #202)

Dear Dr. Luisa Morales-Nebreda,

Thank you for using immunarch! The number of clones is calculated via the number of reads aligned to a specific clonotype or the number of Unique Molecular Identifiers assigned to immune cells. It is possible to reconstruct alpha/beta pairing for overabundant clonotypes using bulk sequencing data. Still, yes, it's much better to use single-cell sequencing if your goal is to analyze paired data.

Would you mind sharing more details on the project you have in mind? We worked with Northwestern on immunotherapy in the past, and we are in the space of combining single-cell transcriptomics and immunomics, so I believe we could help. Please let me know if a call would be more convenient for you rather than a response here.

Best, Vadim

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[vadimnazarov]

Hi Luisa,

I'm sorry for my late response, GitHub didn't send me a notification. I don't see your email on GitHub, would you be willing to reach out to me at [email protected] so we can schedule a meeting? Thank you so much in advance, and I'm sorry for the inconvenience with GitHub!

Best, Vadim