# MiXCR failing to extract VDJ from B cell fastq.gz

**URL:** <https://help.galaxyproject.org/t/mixcr-failing-to-extract-vdj-from-b-cell-fastq-gz/6496>\
**Category:** usegalaxy.eu support\
**Created:** [August 10, 2021, 2:25pm UTC](https://help.galaxyproject.org/t/mixcr-failing-to-extract-vdj-from-b-cell-fastq-gz/6496 "2021-08-10T14:25:53Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![carolyn\_nielsen](https://avatars.discourse-cdn.com/v4/letter/c/edb3f5/32.png) [@carolyn\_nielsen](https://help.galaxyproject.org/u/carolyn_nielsen)\
**Post date:** [August 10, 2021, 2:25pm UTC](https://help.galaxyproject.org/t/mixcr-failing-to-extract-vdj-from-b-cell-fastq-gz/6496/1 "2021-08-10T14:25:53Z")

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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:

 ![image](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/9/9069ececbff64e8ef995607f69dea33b8f9bd8b3.png)

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.  
 ![image](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/e/e18263a21fae17d5f7965586ccb9101f48cb8d41.png)

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?  
 ![image](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/7/748c255fad3597065b59392bc61c369d35bce7b3.png)

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**Author:** ![OrangeOwl23](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/orangeowl23/32/2893_2.png) [@OrangeOwl23](https://help.galaxyproject.org/u/OrangeOwl23)\
**Post date:** [October 28, 2021, 3:00pm UTC](https://help.galaxyproject.org/t/mixcr-failing-to-extract-vdj-from-b-cell-fastq-gz/6496/2 "2021-10-28T15:00:41Z")

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

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**Author:** ![carolyn\_nielsen](https://avatars.discourse-cdn.com/v4/letter/c/edb3f5/32.png) [@carolyn\_nielsen](https://help.galaxyproject.org/u/carolyn_nielsen)\
**Post date:** [October 28, 2021, 3:58pm UTC](https://help.galaxyproject.org/t/mixcr-failing-to-extract-vdj-from-b-cell-fastq-gz/6496/3 "2021-10-28T15:58:59Z")

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

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**Author:** ![gallardoalba](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/gallardoalba/32/1903_2.png) [@gallardoalba](https://help.galaxyproject.org/u/gallardoalba)\
**Post date:** [October 29, 2021, 12:57pm UTC](https://help.galaxyproject.org/t/mixcr-failing-to-extract-vdj-from-b-cell-fastq-gz/6496/4 "2021-10-29T12:57:17Z")

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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

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**Author:** ![Mark\_Izraelson](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/mark_izraelson/32/3999_2.png) [@Mark\_Izraelson](https://help.galaxyproject.org/u/Mark_Izraelson)\
**Post date:** [February 10, 2023, 9:58am UTC](https://help.galaxyproject.org/t/mixcr-failing-to-extract-vdj-from-b-cell-fastq-gz/6496/5 "2023-02-10T09:58:03Z")

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> [@carolyn\_nielsen](#):
>
> SmartSeq

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:

```auto
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:

> **[Built-in presets - MiXCR](https://mixcr.com/mixcr/reference/overview-built-in-presets/#smart-seq2)**
>
> MiXCR: ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.

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

Disclaimer: I am one of the developers of MiXCR