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mixcr exportReadsForClones

Exports raw sequencing reads that were used to build clonotypes from .clna file. Note that such export is possible only from .clna files, produced by MiXCR assemble command with option --write-alignments.

mixcr exportReadsForClones [-fs]
    --id [<ids>...]
    clones.clna
    output.fastq.gz
Output file name will be transformed into _R1/_R2 pair in case of paired end reads.

--id [<ids>...]

list of clonotype ids to export; use -1 to export reads that were not used in clonotypes

-s, --separate

create separate files for each clone. File or pair of _R1/_R2 files, with _clnN suffix, where N is clone index, will be created for each clone index

Extract reads in for specified clonotypes into separate files:

> mixcr exportReadsForClones \
  -s --id 2 12 45 \
  clones.clna \
  reads.fastq.gz

Extract into a single file:

> mixcr exportReadsForClones \
  --id 2 12 45 \
  clones.clna \
  reads.fastq.gz