mixcr exportClonesOverlap

Exports overlap table for a given list of clonesets.

mixcr exportClonesOverlap 
    [--chains <chain>[,<chain>...]]... 
    [--criteria <s>] 
    [--only-productive] 
    [--not-covered-as-empty]
    [<exportField>]...
    [--force-overwrite]
    [--no-warnings] 
    [--verbose]
    [--help]
    cloneset.(clns|clna)... output.tsv

The resulting tab-delimited .tsv table contains:

• "overlap" columns corresponding to the criteria used for overlap and common for all samples
• other export columns that are not used in the overlap for each of the sample individually

Since the resulting .tsv table may be rather large, MiXCR by default exports only overlap columns and clonotype counts and fractions in each of the samples. One can specify additional columns to export per cloneset using standard MiXCR notation used in exportClones command.

Other command line options are:

cloneset.(clns|clna)...

Paths to input files

output.tsv

Path template where to write output export tables. For each chain will be generated table with path {outputDir}/{outputFileName}.{chain}.tsv

--chains <chain>[,<chain>...]

Output overlap for specified chains only; if multiple chains are specified, results per each chains will be exported in separate files.

--criteria <s>

Overlap criteria. Defines the rules to treat clones as equal. It allows to specify gene feature for overlap (nucleotide or amino acid), and optionally use V and J hits. Examples: CDR3|AA|V|J (overlap by a.a. CDR3 and V and J), VDJRegion|AA (overlap by a.a. VDJRegion), CDR3|NT|V (overlap by nt CDR3 and V). Default: CDR3|AA|V|J

--only-productive

Filter out-of-frame sequences and clonotypes with stop-codons

--not-covered-as-empty

Export not covered regions as empty text.

-f, --force-overwrite

Force overwrite of output file(s).

-nw, --no-warnings

Suppress all warning messages.

--verbose

Verbose messages.

-h, --help

Show this help message and exit.

<exportField>

A list of export fields for clones.

Example

Build and export overlap for TRA/TRD chain:

> mixcr exportClonesOverlap \
  --chains TRAD \
  --only-productive \
  --criteria "CDR3|AA|V|J" \
  clonesets/*.clns
  overlapTable.tsv 

The resulting table:

Here column nSamples is number of samples containing the clonotype and columns samplei_countAggregated — sum of the counts of all clonotypes in samplei with this amino acid sequence, V- and J-gene assignments.