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
Other command line options are:
- Paths to input files
- Path template where to write output export tables. For each
chainwill be generated table with path
- Output overlap for specified chains only; if multiple chains are specified, results per each chains will be exported in separate files.
- 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.
CDR3|NT|V(overlap by nt CDR3 and V). Default: CDR3|AA|V|J
- Filter out-of-frame sequences and clonotypes with stop-codons
- Export not covered regions as empty text.
- Force overwrite of output file(s).
- Suppress all warning messages.
- Verbose messages.
- Show this help message and exit.
- A list of export fields for clones.
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:
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.