MiXCR: only create a single export file for all clonotypes 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?
This is from the MiXCR documentation:

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


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.