`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