Answers.Body: <p>Currently in MiXCR SERIES 4 you can use <code>--dont-split-files </code> parameter here.
  Please check our new documentation portal:
  <a href="https://docs.milaboratories.com/mixcr/reference/mixcr-export/#clonotype-tables" rel="nofollow noreferrer">https://docs.milaboratories.com/mixcr/reference/mixcr-export/#clonotype-tables</a></p>
  <p>Also now we support presets that allow to perform analysis for a lot of standard protocols using a one line command.</p>
  
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Answers.LastActivityDate: 2023-01-24T15:15:05.500Z
Answers.UserDisplayName: Mark Izraelson
Answers.Body: <p>After finding the correct entry in the MiXCR documentation (thanks to haci), I learned that the parameter <code>--receptor-type</code> is responsible for which sequences will be returned.</p>
  
  <p>The default for this parameter when using mixcr analyze is <code>--receptor-type xcr</code>, and stands for 'all chains', thus returning such a vast output. Changing this parameter to e.g. BCR solved my issue.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-11T12:27:49.673Z
Answers.Text: Where can I find the default value for the --receptor-type parameter? I cannot find it in the manual, can you please point out the relevant section?
Answers.UserDisplayName: haci
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Answers.Text: I found it in the analyze section of the [MiXCR docs](https://mixcr.readthedocs.io/en/master/analyze.html), under the optional parameters.
Answers.UserDisplayName: Jan
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Answers.CreationDate: 2019-09-11T11:25:15.443Z
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Answers.UserDisplayName: Jan
Answers.Body: <p>This is from the <a href="https://buildmedia.readthedocs.org/media/pdf/mixcr/develop/mixcr.pdf" rel="nofollow noreferrer">MiXCR documentation</a>:</p>
  
  <pre><code>Under the hood analyze amplicon is equivalent to the execution of the following
  MiXCR actions options:
  &gt; mixcr align -s hs -p kAligner2 input_R1.fastq input_R2.fastq alignments.vdjca
  ... Building alignments
  &gt; mixcr assemble alignments.vdjca clones.clns
  ... Assembling clones
  &gt; mixcr exportClones --chains IGH clones.clns clones.txt
  ... Exporting clones to tab-delimited file
  </code></pre>
  
  <p>So when using <code>analyze amplicon</code>, you are using <code>mixcr exportClones</code> under the hood and not <code>exportAlignments</code>, hence the difference in output.</p>
  
  <p>I believe what you are experiencing results from a bug, please see this <a href="https://github.com/milaboratory/mixcr/issues/454" rel="nofollow noreferrer">issue</a>. If this is the case, all these files should be the same according to the bug report. Fortunately the developers have already addressed the bug in version 3.0.3.</p>
  
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Answers.Text: As I was already running version 3.0.9 of mixcr, the bug you found (which corresponds to my observation) should have been fixed. However, although running `mixcr exportClones prefix.clna clones.txt` returns only one file as expected, the same is not true for me when using the `analyze amplicon` command. So, even though those commands are supposed to be equivalent, their output suggests otherwise for me.
Answers.UserDisplayName: Jan
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Answers.LastActivityDate: 2019-09-10T19:32:02.567Z
Answers.LastEditDate: 2019-09-10T19:32:02.567Z
Answers.UserDisplayName: haci
Body: <p>I am using following command from MiXCR to both align, assemble and export my input files:</p>
  
  <pre><code>mixcr analyze amplicon \
      -s hsa \
      --starting-material rna \
      --5-end no-v-primers \
      --3-end c-primers \
      --adapters adapters-present \
      --export "-aaFeature CDR1 -nFeature CDR1 -aaFeature CDR2 \
                -nFeature CDR2 -aaFeature CDR3 -nFeature CDR3 \
                -aaFeature VGene -cGenes -count" \
      --assemble "-OassemblingFeatures=[CDR1,CDR2,CDR3]" \
      INPUT_FILE.fasta analysis_name
  </code></pre>
  
  <p>Unfortunately, this creates multiple output file (analysis_name.clonotypes.ALL.txt, analysis_name.clonotypes.IGH.txt, etc.), which stands in contrast to the output of the <code>mixcr exportAlignments</code> command.</p>
  
  <p>How can I export a single txt file instead, while still using the <code>mixcr analyze</code> command?</p>
  
Tags: <phylogenetics><fasta><bash>
Title: MiXCR: only create a single export file for all clonotypes
ThreadText: # MiXCR: only create a single export file for all clonotypes
  
  (Asked by: username_0 on 2019-09-10)
  
  I am using following command from MiXCR to both align, assemble and export my input files:
  
  ```
  mixcr analyze amplicon \
      -s hsa \
      --starting-material rna \
      --5-end no-v-primers \
      --3-end c-primers \
      --adapters adapters-present \
      --export "-aaFeature CDR1 -nFeature CDR1 -aaFeature CDR2 \
                -nFeature CDR2 -aaFeature CDR3 -nFeature CDR3 \
                -aaFeature VGene -cGenes -count" \
      --assemble "-OassemblingFeatures=[CDR1,CDR2,CDR3]" \
      INPUT_FILE.fasta analysis_name
  
  ```
  
  Unfortunately, this creates multiple output file (analysis\_name.clonotypes.ALL.txt, analysis\_name.clonotypes.IGH.txt, etc.), which stands in contrast to the output of the `mixcr exportAlignments` command.
  
  How can I export a single txt file instead, while still using the `mixcr analyze` command?
  
  **Tags:** phylogenetics, fasta, bash
  
  
  ---
  
  ## 3 answers
  
  ### Answer by username_2 on 2019-09-10. Score: 3 | Accepted answer
  
  This is from the [MiXCR documentation](https://buildmedia.readthedocs.org/media/pdf/mixcr/develop/mixcr.pdf):
  
  ```
  Under the hood analyze amplicon is equivalent to the execution of the following
  MiXCR actions options:
  > mixcr align -s hs -p kAligner2 input_R1.fastq input_R2.fastq alignments.vdjca
  ... Building alignments
  > mixcr assemble alignments.vdjca clones.clns
  ... Assembling clones
  > mixcr exportClones --chains IGH clones.clns clones.txt
  ... Exporting clones to tab-delimited file
  
  ```
  
  So when using `analyze amplicon`, you are using `mixcr exportClones` under the hood and not `exportAlignments`, hence the difference in output.
  
  I believe what you are experiencing results from a bug, please see this [issue](https://github.com/milaboratory/mixcr/issues/454). If this is the case, all these files should be the same according to the bug report. Fortunately the developers have already addressed the bug in version 3.0.3.
  
  > **Comments:**
  > **username_0**: As I was already running version 3.0.9 of mixcr, the bug you found (which corresponds to my observation) should have been fixed. However, although running `mixcr exportClones prefix.clna clones.txt` returns only one file as expected, the same is not true for me when using the `analyze amplicon` command. So, even though those commands are supposed to be equivalent, their output suggests otherwise for me.  
  
  ---
  
  ### Answer by username_1 on 2023-01-24. Score: 3
  
  Currently in MiXCR SERIES 4 you can use `--dont-split-files`  parameter here.
  Please check our new documentation portal:
  <https://docs.milaboratories.com/mixcr/reference/mixcr-export/#clonotype-tables>
  
  Also now we support presets that allow to perform analysis for a lot of standard protocols using a one line command.
  
  
  ---
  
  ### Answer by username_0 on 2019-09-11. Score: 2
  
  After finding the correct entry in the MiXCR documentation (thanks to username_2), I learned that the parameter `--receptor-type` is responsible for which sequences will be returned.
  
  The default for this parameter when using mixcr analyze is `--receptor-type xcr`, and stands for 'all chains', thus returning such a vast output. Changing this parameter to e.g. BCR solved my issue.
  
  > **Comments:**
  > **username_2**: Where can I find the default value for the --receptor-type parameter? I cannot find it in the manual, can you please point out the relevant section?  
  > **username_0**: I found it in the analyze section of the [MiXCR docs](https://mixcr.readthedocs.io/en/master/analyze.html), under the optional parameters.  
  
  ---
  
  