text: user5186: 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?
  
  user5186: After finding the correct entry in the MiXCR documentation (thanks to haci), 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.
  
  user3541: This is from the MiXCR documentation:
  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. 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.
  
  user16818: 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.
  
original_text: 5186: <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>
   5186: <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>
   3541: <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>
   16818: <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>
  