MiXCR failing to extract VDJ from B cell fastq.gz

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1

I am trying to extract BCR data from single (B) cell RNA sequencing data (SmartSeq, Nextera, HiSeq4000) to compare clonotypes between two samples. I’m particularly interested in comparing % germline mutation to look at affinity maturation.

These are the settings I have used:

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I have tried running one of my samples (= 81 paired reads, i.e. 81 B cells) with MiXCR with the shotgun analyze approach for non-enriched libraries, and it seems to run without any errors but all the clonotype tables are empty.
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The report for the same sample shows this in the final section which makes it look like contigs have been generated. Could you please advise how to get these to export?
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2

I’m having the same issue here. Have you had any luck since posting this?

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Unfortunately not in Galaxy - my bioinformatician collaborator ended up running MiXCR himself.

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Hi @carolyn_nielsen,
sorry for the late response; I asked @OrangeOwl23 to share their datasets with me in order to reproduce the problem. I’ll try to fix it as soon as possible.

Regards

5

Hi, also MiXCR now supports SmartSeq2 protocol out of the box (and other single-cell protocols). There is a single command that only requires to set the species and provide input files:

mixcr analyze smartseq2-vdj-full-length \
    -s hsa \
    161014_SN163_0729_AH3VW7BCXY_L1_{{CELL0ROW:a}}-{{CELL0COL:a}}_R1.fastq.gz \
    161014_SN163_0729_AH3VW7BCXY_L1_{{CELL0ROW:a}}-{{CELL0COL:a}}_R2.fastq.gz \
    result

You can read more on that here:

Also, let me know if you need any help running the software.

Disclaimer: I am one of the developers of MiXCR

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