Export

Export clonotypes or raw alignments in a tabular form.

MiXCR uses highly efficient binary formats that hold exhaustive information on the clonotypes, alignments, barcodes and original sequencing reads:

• .vdjca produced by align and holds alignments
• .clns produced by assemble and assembleContigs holds clonotypes
• .clna produced by assemble and holds both clonotypes and alignments

MiXCR provides functions for export alignments, clonotype tables in a tab-delimited way. For human-readable formatted output see pretty export.

For export of .shmt produced by findShmTrees see exportShmTrees.md.

Clonotype tables

mixcr exportClones
    [--chains <chains>] 
    [--filter-out-of-frames] 
    [--filter-stops] 
    [--split-by-tags <(Molecule|Cell|Sample)>] 
    [--split-files-by <splitFilesBy>]... 
    [--dont-split-files] 
    [--impute-germline-on-export] 
    [--dont-impute-germline-on-export] 
    [--add-export-clone-table-splitting <(geneLabel|tag):key>] 
    [--reset-export-clone-table-splitting] 
    [--add-export-clone-grouping <(geneLabel|tag):key>] 
    [--reset-export-clone-grouping] 
    [--export-productive-clones-only] 
    [--no-header] 
    [--drop-default-fields] 
    [--prepend-columns] 
    [--not-covered-as-empty]
    [<exportField>]...
    [--force-overwrite] 
    [--no-warnings] 
    [--verbose] 
    [--help] 
    data.(clns|clna) [table.tsv]

Exports tab-delimited table of alignments from .clns and .clna files.

Command line options:

data.(clns|clna)

Path to input file with clones

[table.tsv]

Path where to write export table. Will write to output if omitted.

-c, --chains <chains>

Limit export to specific chain (e.g. TRA or IGH) (fractions will be recalculated). Default value determined by the preset.

-o, --filter-out-of-frames

Exclude clones with out-of-frame clone sequences (fractions will be recalculated). Default value determined by the preset.

-t, --filter-stops

Exclude sequences containing stop codons (fractions will be recalculated). Default value determined by the preset.

--split-by-tags <(Molecule|Cell|Sample)>

Split clones by tag type. Will be calculated from export columns if not specified. Default value determined by the preset.

--split-files-by <splitFilesBy>

Split files by (currently the only supported value is "geneLabel:reliableChain" etc... ). Default value determined by the preset.

--dont-split-files

Don't split files.

--impute-germline-on-export

Export nucleotide sequences using letters from germline (marked lowercase) for uncovered regions

--dont-impute-germline-on-export

Export nucleotide sequences only from covered region

--add-export-clone-table-splitting <(geneLabel|tag):key>

Add key to split output files with clone tables.

--reset-export-clone-table-splitting

Reset all file splitting for output clone tables.

--add-export-clone-grouping <(geneLabel|tag):key>

Add key to group clones in the output clone tables.

--reset-export-clone-grouping

Reset all clone grouping in the output clone tables.

--export-productive-clones-only

Export only productive clonotypes.

--no-header

Don't print first header line, print only data Default value determined by the preset.

--drop-default-fields

Don't export fields from preset.

--prepend-columns

Added columns will be inserted before default columns. By default columns will be added after default columns

--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

Clone groups by cell

mixcr exportCloneGroups
    [--filter-out-of-frames]
    [--filter-stops]
    [--filter-groups-with-one-chain]
    [--impute-germline-on-export]
    [--dont-impute-germline-on-export]
    [--export-productive-clones-only]            
    [--export-clone-groups-for-cell-type <cell_type>...]...
    [--export-clone-groups-for-all-cell-types]
    [--show-secondary-chain-on-export-cell-groups <type> ]
    [--dont-show-secondary-chain-on-export-cell-groups] 
    [--no-header]
    [--drop-default-fields]
    [<exportField>]...
    [--prepend-columns]
    [--not-covered-as-empty]
    [--force-overwrite]
    [--no-warnings]
    [--verbose]
    [--help] 
    data.(clns|clna)
    [table.tsv]

Exports information about clonotypes combined by Cell tag. Input .clns/.clna files have to be grouped with mixcr groupClones.

Command line options:

data.(clns|clna)

Path to input file with clones

[table.tsv]

Path where to write export table. Will write to output if omitted.

--filter-out-of-frames

Exclude clones with out-of-frame clone sequences (fractions will be recalculated). Default value determined by the preset.

--filter-stops

Exclude sequences containing stop codons (fractions will be recalculated). Default value determined by the preset.

--filter-groups-with-one-chain

Exclude groups containing only one clone (fractions will be recalculated). Default value determined by the preset.`

--impute-germline-on-export

Export nucleotide sequences using letters from germline (marked lowercase) for uncovered regions

--dont-impute-germline-on-export

Export nucleotide sequences only from covered region

--export-productive-clones-only

Export only productive clonotypes.

--export-clone-groups-for-cell-type <cell_type>...

Export clone groups for given cell type. Possible values: IGH-IGK, IGH-IGL, TRB-TRA, TRD-TRG

--export-clone-groups-for-all-cell-types

Export clone groups for all cell types.

--show-secondary-chain-on-export-cell-groups <type>

Show columns for secondary chains in export for cell groups. Possible values to decide the weight: read, molecule, auto.

--dont-show-secondary-chain-on-export-cell-groups

Don't show columns for secondary chains in export for cell groups.

--no-header

Don't print first header line, print only data Default value determined by the preset.

--drop-default-fields

Don't export fields from preset.

--prepend-columns

Added columns will be inserted before default columns. By default columns will be added after default columns

--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

Alignments

mixcr exportAlignments
    [--chains <chains>] 
    [--impute-germline-on-export]
    [--dont-impute-germline-on-export] 
    [--no-header] 
    [--drop-default-fields] 
    [--prepend-columns] 
    [--not-covered-as-empty]
    [<exportField>]...
    [--force-overwrite] 
    [--no-warnings] 
    [--verbose] 
    [--help] 
    data.(vdjca|clns|clna) [table.tsv]

Exports tab-delimited alignments from .vdjca, .clns and .clna files.

Command line options:

data.[vdjca|clns|clna]

Path to input file

[table.tsv]

Path where to write export table. Will write to output if omitted.

-c, --chains <chains>

Limit export to specific chain (e.g. TRA or IGH) (fractions will be recalculated) Default value determined by the preset.

--impute-germline-on-export

Export nucleotide sequences using letters from germline (marked lowercase) for uncovered regions

--dont-impute-germline-on-export

Export nucleotide sequences only from covered region

--no-header

Don't print first header line, print only data Default value determined by the preset.

--drop-default-fields

Don't export fields from preset.

--prepend-columns

Added columns will be inserted before default columns. By default columns will be added after default columns

--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

Examples

Default export

> mixcr exportClones clones.clns clones.tsv

The resulting tab-delimited text file will contain default set of columns (determined by the used preset) which includes clonotype abundances, nucleotide and amino acid clonotype sequences, Phred qualities, all or just best hit for V, D, J and C genes, corresponding alignments, nucleotide and amino acid sequences of gene regions present in sequence, etc. Example output (for BCR full-length data):

One can customize the list of fields that will be exported. For example, in order to export just clone count, best hits for V and J genes with corresponding alignments and CDR3 amino acid sequence, one can do:

> mixcr exportClones \
    --drop-default-fields \
    -count \
    -vHit -jHit \
    -vAlignment -jAlignment \
    -aaFeature CDR3 \
    clones.clns \
    clones.tsv

The columns in the resulting file will be exported in exactly the same order as parameters on the command line.

UMI libraries

> mixcr exportClones \
    -uniqueTagCount Molecule \
    clones.clns \
    clones.tsv

There are several options to export columns related to tagged analysis. In the above example we pass -uniqueTagCount option to add a column with UMI count. We also specify option to use full preset of other columns.

It is also possible to export full list of UMIs with their read counts that were used to build a clonotype:

> mixcr exportClones \
    -uniqueTagCount Molecule \
    -tagCounts \
    clones.clns \
    clones.tsv

Single cell libraries

Export paired TCR-alpha/beta or BCR-heavy/light clonotype pairs from single cell data:

> mixcr exportClones \
    --drop-default-fields \
    --split-by-tags Cell \
    -tag cell \
    -cellGroup \
    -uniqueTagCount Molecule \
    -count \
    -vFamily -jFamily \
    -aaFeature CDR3 \
    -nFeatureImputed VDJRegion \
    clones.clns \
    clones.tsv

Here we use --split-by-tags option to export cells that contain the same clonotype on separate rows, -tags to export cell barcode for each clonotype and -cellGroup which is cell identifier.

In the above example we specified particular columns to export. To export all columns one can use simply:

> mixcr exportClones \
    --split-by-tags Cell \
    -tag cell \
    -cellGroup \
    -uniqueTagCount Molecule \
    clones.clns \
    clones.tsv

Export contigs with imputation

When V-D-J contigs assembled with assembleContigs does not cover all gene features, it still might be useful to impute non-covered parts from germline (for example for the purposes of synthesis). Typically, there may be uncovered parts in VDJRegion for example due to long CDR3 region and non-overlapping R1 or R2, or in case of fragmented data (RNA-Seq or 10x single cell).

> mixcr exportClones \
    -aaFeatureImputed VDJRegion \
    -nFeatureImputed VDJRegion \
    clones.clns clones.tsv  

MiXCR allows to export gene features with imputation using -nFeatureImputed and -aaFeatureImputed export fields. The resulting sequences will have imputed letters in lower case:

One can also use default presets with imputation (all gene features will use imputation option):

> mixcr exportClones \
    --drop-default-fields \
    -aaFeatureImputed VDJRegion \
    -nFeatureImputed VDJRegion \
    clones.clns clones.tsv  

Export fields

Common fields

These fields available for exportAlignments and exportClones:

-targets

Export number of targets

-vHit

Export best V hit

-dHit

Export best D hit

-jHit

Export best J hit

-cHit

Export best C hit

-vGene

Export best V hit gene name (e.g. TRBV12-3 for TRBV12-3*00)

-dGene

Export best D hit gene name (e.g. TRBV12-3 for TRBV12-3*00)

-jGene

Export best J hit gene name (e.g. TRBV12-3 for TRBV12-3*00)

-cGene

Export best C hit gene name (e.g. TRBV12-3 for TRBV12-3*00)

-vFamily

Export best V hit family name (e.g. TRBV12 for TRBV12-3*00)

-dFamily

Export best D hit family name (e.g. TRBV12 for TRBV12-3*00)

-jFamily

Export best J hit family name (e.g. TRBV12 for TRBV12-3*00)

-cFamily

Export best C hit family name (e.g. TRBV12 for TRBV12-3*00)

-vHitScore

Export score for best V hit

-dHitScore

Export score for best D hit

-jHitScore

Export score for best J hit

-cHitScore

Export score for best C hit

-vHitsWithScore

Export all V hits with score

-dHitsWithScore

Export all D hits with score

-jHitsWithScore

Export all J hits with score

-cHitsWithScore

Export all C hits with score

-vHits

Export all V hits

-dHits

Export all D hits

-jHits

Export all J hits

-cHits

Export all C hits

-vGenes

Export all V gene names (e.g. TRBV12-3 for TRBV12-3*00)

-dGenes

Export all D gene names (e.g. TRBV12-3 for TRBV12-3*00)

-jGenes

Export all J gene names (e.g. TRBV12-3 for TRBV12-3*00)

-cGenes

Export all C gene names (e.g. TRBV12-3 for TRBV12-3*00)

-vFamilies

Export all V gene family anmes (e.g. TRBV12 for TRBV12-3*00)

-dFamilies

Export all D gene family anmes (e.g. TRBV12 for TRBV12-3*00)

-jFamilies

Export all J gene family anmes (e.g. TRBV12 for TRBV12-3*00)

-cFamilies

Export all C gene family anmes (e.g. TRBV12 for TRBV12-3*00)

-vAlignment

Export best V alignment

-dAlignment

Export best D alignment

-jAlignment

Export best J alignment

-cAlignment

Export best C alignment

-vAlignments

Export all V alignments

-dAlignments

Export all D alignments

-jAlignments

Export all J alignments

-cAlignments

Export all C alignments

-qFeature <gene_feature>

Export quality string of specified gene feature

-nFeatureImputed <gene_feature>

Export nucleotide sequence of specified gene feature using letters from germline (marked lowercase) for uncovered regions

-allNFeaturesImputed [<from_reference_point> <to_reference_point>]

Export nucleotide sequence using letters from germline (marked lowercase) for uncovered regions for all gene features between specified reference points (in separate columns).

For example, -allNFeaturesImputed FR3Begin FR4End will export -nFeatureImputed FR3, -nFeatureImputed CDR3, -nFeatureImputed FR4.

By default, boundaries will be got from analysis parameters if possible or FR1Begin FR4End otherwise.

-aaFeatureImputed <gene_feature>

Export amino acid sequence of specified gene feature using letters from germline (marked lowercase) for uncovered regions

-allAAFeaturesImputed [<from_reference_point> <to_reference_point>]

Export amino acid sequence using letters from germline (marked lowercase) for uncovered regions for all gene features between specified reference points (in separate columns).

For example, -allAAFeaturesImputed FR3Begin FR4End will export -aaFeatureImputed FR3, -aaFeatureImputed CDR3, -aaFeatureImputed FR4.

By default, boundaries will be got from analysis parameters if possible or FR1Begin FR4End otherwise.

-minFeatureQuality <gene_feature>

Export minimal quality of specified gene feature

-allMinFeaturesQuality [<from_reference_point> <to_reference_point>]

Export minimal quality for all gene features between specified reference points (in separate columns).

For example, -allMinFeaturesQuality FR3Begin FR4End will export -minFeatureQuality FR3, -minFeatureQuality CDR3, -minFeatureQuality FR4.

By default, boundaries will be got from analysis parameters if possible or FR1Begin FR4End otherwise.

-allNFeaturesWithMinQuality [<from_reference_point> <to_reference_point>]

Export nucleotide sequences and minimal quality for all gene features between specified reference points (in separate columns).

For example, -allNFeaturesWithMinQuality FR3Begin FR4End will export -nFeature FR3, -minFeatureQuality FR3, -nFeature CDR3, -minFeatureQuality CDR3, -nFeature FR4, -minFeatureQuality FR4.

By default, boundaries will be got from analysis parameters if possible or FR1Begin FR4End otherwise.

-allNFeaturesImputedWithMinQuality [<from_reference_point> <to_reference_point>]

Export nucleotide sequences and minimal quality for all gene features between specified reference points (in separate columns).

For example, -allNFeaturesImputedWithMinQuality FR3Begin FR4End will export -nFeatureImputed FR3, -minFeatureQuality FR3, -nFeatureImputed CDR3, -minFeatureQuality CDR3, -nFeatureImputed FR4, -minFeatureQuality FR4.

By default, boundaries will be got from analysis parameters if possible or FR1Begin FR4End otherwise.

-avrgFeatureQuality <gene_feature>

Export average quality of specified gene feature

-allAvrgFeaturesQuality [<from_reference_point> <to_reference_point>]

Export average quality for all gene features between specified reference points (in separate columns).

For example, -allAvrgFeaturesQuality FR3Begin FR4End will export -avrgFeatureQuality FR3, -avrgFeatureQuality CDR3, -avrgFeatureQuality FR4.

By default, boundaries will be got from analysis parameters if possible or FR1Begin FR4End otherwise.

-nLength <gene_feature> [germline]

Export length of specified gene feature in nucleotides. If second option is germline than will be count corresponding top genes, VJJunction will be excluded from calculation (germline is unknown). It's recommended to run findAlleles before exporting -nLength<gene_feature> germline because otherwise germline sequence will not incorporate allelic mutations. For clones from all chains.

-allNLength [<from_reference_point> <to_reference_point>]

Export length for all gene features between specified reference points (in separate columns) in nucleotides.

For example, -allNLength FR3Begin FR4End will export -nLength FR3, -nLength CDR3, -nLength FR4.

By default, boundaries will be got from analysis parameters if possible or FR1Begin FR4End otherwise.

-aaLength <gene_feature> [germline]

Export length of specified gene feature in amino acids. If second option is germline than will be count corresponding top genes, CDR3 will be excluded from calculation (VJJunction germline is unknown). It's recommended to run findAlleles before exporting-aaLength <gene_feature> germline because otherwise germline sequence will not incorporate allelic mutations.

-allAALength [<from_reference_point> <to_reference_point>]

Export length for all gene features between specified reference points (in separate columns) in amino acids.

For example, -allAALength FR3Begin FR4End will export -aaLength FR3, -aaLength CDR3, -aaLength FR4.

By default, boundaries will be got from analysis parameters if possible or FR1Begin FR4End otherwise.

-nFeature <gene_feature> [germline]

Export nucleotide sequence of specified gene feature. If second option is germline than will be exported corresponded sequence of the top gene. It's recommended to run findAlleles before exporting -nFeature <gene_feature> germline because otherwise germline sequence will not incorporate allelic mutations. For clones from all chains.

-allNFeatures [<from_reference_point> <to_reference_point>]

Export nucleotide sequences for all gene features between specified reference points (in separate columns).

For example, -allNFeatures FR3Begin FR4End will export -nFeature FR3, -nFeature CDR3, -nFeature FR4.

By default, boundaries will be got from analysis parameters if possible or FR1Begin FR4End otherwise.

-aaFeature <gene_feature> [germline]

Export amino acid sequence of specified gene feature. If second option is germline than will be exported corresponded sequence of the top gene. It's recommended to run findAlleles before exporting -aaFeature <gene_feature> germline because otherwise germline sequence will not incorporate allelic mutations. For clones from all chains.

-allAAFeatures [<from_reference_point> <to_reference_point>]

Export amino acid sequence for all gene features between specified reference points (in separate columns).

For example, -allAAFeatures FR3Begin FR4End will export -aaFeature FR3, -aaFeature CDR3, -aaFeature FR4.

By default, boundaries will be got from analysis parameters if possible or FR1Begin FR4End otherwise.

-nMutations <gene_feature> [(substitutions|indels|inserts|deletions)]

Extract nucleotide mutations for specific gene feature; relative to germline sequence. By default, will export all mutations. Can specify the mutation type using the following parameters: substitutions,indels,inserts,deletions.

-allNMutations [<from_reference_point> <to_reference_point>] [(substitutions|indels|inserts|deletions)]

Extract nucleotide mutations relative to germline sequence for all gene features between specified reference points (in separate columns). By default, boundaries will be got from analysis parameters if possible or FR1Begin FR4End otherwise. By default, will export all mutations. Can specify the mutation type using the following second parameter: substitutions,indels,inserts,deletions.

For example, -allNMutations FR3Begin FR4End substitutions will export -nMutations FR3 substitutions, -nMutations FR4 substitutions.

-nMutationsRelative <gene_feature> <relative_to_gene_feature> [(substitutions|indels|inserts|deletions)]

Extract nucleotide mutations for specific gene feature relative to another feature. By default, will export all mutations. Can specify the mutation type using the following parameters: substitutions,indels,inserts,deletions.

-aaMutations <gene_feature> [(substitutions|indels|inserts|deletions)]

Extract amino acid mutations for specific gene feature. By default, will export all mutations. Can specify the mutation type using the second parameters: substitutions,indels,inserts,deletions.

-allAAMutations [<from_reference_point> <to_reference_point>] [(substitutions|indels|inserts|deletions)]

Extract amino acid nucleotide mutations relative to germline sequence for all gene features between specified reference points (in separate columns). Can specify the mutation type using the second parameters: substitutions,indels,inserts,deletions.

For example, -allAAMutations FR3Begin FR4End indels will export -aaMutations FR3 indels, -aaMutations FR4 indels.

By default, boundaries will be got from analysis parameters if possible or FR1Begin FR4End otherwise.

-aaMutationsRelative <gene_feature> <relative_to_gene_feature> [(substitutions|indels|inserts|deletions)]

Extract amino acid mutations for specific gene feature relative to another feature. If no second parameter specified will export all types of mutation. Can specify the mutation type using the second parameters: substitutions,indels,inserts,deletions.

-mutationsDetailed <gene_feature>

Detailed list of nucleotide and corresponding amino acid mutations. Format <nt_mutation>:<aa_mutation_individual>:<aa_mutation_cumulative>, where <aa_mutation_individual> is an expected amino acid mutation given no other mutations have occurred, and <aa_mutation_cumulative> amino acid mutation is the observed amino acid mutation combining effect from all others.

-allMutationsDetailed [<from_reference_point> <to_reference_point>]

Detailed list of nucleotide and corresponding amino acid mutations for all gene features between specified reference points (in separate columns).

For example, -allMutationsDetailed FR3Begin FR4End will export -mutationsDetailed FR3, -mutationsDetailed FR4.

By default, boundaries will be got from analysis parameters if possible or FR1Begin FR4End otherwise.

-mutationsDetailedRelative <gene_feature> <relative_to_gene_feature>

Detailed list of nucleotide and corresponding amino acid mutations written, positions relative to specified gene feature. Format ::, where is an expected amino acid mutation given no other mutations have occurred, and amino acid mutation is the observed amino acid mutation combining effect from all others. WARNING: format may change in following versions.

-nMutationsCount <gene_feature> [(substitutions|indels|inserts|deletions)]

Export the number of mutations in specified gene feature. If no second parameter specified will export all types of mutation. Can specify the mutation type using the second parameters: substitutions,indels,inserts,deletions.

-allNMutationsCount [<from_reference_point> <to_reference_point>] [(substitutions|indels|inserts|deletions)]

Count nucleotide mutations for all gene features between specified reference points (in separate columns). For example, -allNMutationsCount FR3Begin FR4End will export-nMutationsCount FR3, -nMutationsCount CDR3, -nMutationsCount FR4. By default, boundaries will be got from analysis parameters if possible or FR1Begin FR4End otherwise. If no second parameter specified will export all types of mutation. Can specify the mutation type using the second parameters: substitutions,indels,inserts,deletions.

-aaMutationsCount <gene_feature> [(substitutions|indels|inserts|deletions)]

Count amino acid mutations for specific gene feature. If no second parameter specified will export all types of mutation. Can specify the mutation type using the second parameters: substitutions,indels,inserts,deletions.

-allAAMutationsCount [<from_reference_point> <to_reference_point>] [(substitutions|indels|inserts|deletions)]

Count amino acid mutations for all gene features between specified reference points (in separate columns). For example, -allAAMutationsCount FR3Begin FR4End will export-aaMutationsCount FR3, -aaMutationsCount CDR3,-aaMutationsCount FR4. By default, boundaries will be got from analysis parameters if possible or FR1Begin FR4End otherwise. If no second parameter specified will export all types of mutation. Can specify the mutation type using the second parameters: substitutions,indels,inserts,deletions.

-nMutationRate <gene_feature> [(substitutions|indels|inserts|deletions)]

Number of mutations from germline divided by target sequence size. VJJunction is excluded from calculation (as germline is undefined). It's recommended to run findAlleles before exporting -mutationRate because otherwise mutations count will include allelic mutations. If no second parameter specified will export all types of mutation. Can specify the mutation type using the second parameters: substitutions,indels,inserts,deletions.

-aaMutationRate <gene_feature> [(substitutions|indels|inserts|deletions)]

Number of amino acid mutations from germline divided by amino acid sequence size. CDR3 is excluded from calculation (as VJJunction germline is undefined). It's recommended to run findAlleles before exporting -aaMutationRate because otherwise mutations count will include allelic mutations. If no second parameter specified will export all types of mutation. Can specify the mutation type using the second parameters: substitutions,indels,inserts,deletions.

-positionInReferenceOf <reference_point>

Export position of specified reference point inside reference sequences (clonal sequence / read sequence).

-allPositionsInReference [<from_reference_point> <to_reference_point>]

Export position inside reference sequences (clonal sequence / read sequence) for all reference points between specified (in separate columns).

For example, -allPositionsInReference FR3Begin FR4End will export -positionInReferenceOf FR3Begin, -positionInReferenceOf CDR3Begin, -positionInReferenceOf CDR3End and -positionInReferenceOf FR4End.

By default, boundaries will be got from analysis parameters if possible or FR1Begin FR4End otherwise.

-positionOf <reference_point>

Export position of specified reference point inside target sequences (clonal sequence / read sequence).

-allPositions [<from_reference_point> <to_reference_point>]

Export position inside target sequences (clonal sequence / read sequence) for all reference points between specified (in separate columns).

For example, -allPositions FR3Begin FR4End will export -positionOf FR3Begin, -positionOf CDR3Begin, -positionOf CDR3End and -positionOf FR4End.

By default, boundaries will be got from analysis parameters if possible or FR1Begin FR4End otherwise.

-defaultAnchorPoints

Outputs a list of default reference points (like CDR2Begin, FR4End, etc. see documentation bellow for the full list and formatting)

-targetSequences

Export aligned sequences (targets), separated with comma

-targetQualities

Export aligned sequence (target) qualities, separated with comma

-vIdentityPercents

V alignment identity percents

-dIdentityPercents

D alignment identity percents

-jIdentityPercents

J alignment identity percents

-cIdentityPercents

C alignment identity percents

-vBestIdentityPercent

V best alignment identity percent

-dBestIdentityPercent

D best alignment identity percent

-jBestIdentityPercent

J best alignment identity percent

-cBestIdentityPercent

C best alignment identity percent

-chains

Chains

-isotype [(primary|subclass|auto)]

Export isotype for IGH chains if it's distinguishable. primary will resolve 'IgA', 'IgD', 'IgG', 'IgE', 'IgM'. subtype will try resolve isotypes like 'IgA1' or 'IgA2'. Default auto will automatically decide whether to resolve the primary or subtype isotype based on the level of detail distinguishable for each clone.

-topChains

Top chains

-geneLabel <label>

Export gene label (i.e. ReliableChain)

-tagCounts

All tags with counts

-tags <(Molecule|Cell|Sample)>

All tags values (i.e. CELL barcode or UMI sequence).

-uniqueTagCount <(Molecule|Cell|Sample)>

Unique tag count. Tag type will be used for filtering tags for export.

-cellId [<(none|space|dash)>]

Concatenated all cell tags with specified delimiter, default delimiter is none. Example output for -cellId: GGATTACTCATTGCCC, for -cellId dash: GGATTACT-CATTGCCC.

-isOOF <geneFeature>

Whether specified gene feature is out of frame.

-hasStops <geneFeature>

Whether specified gene contains stop codons.

-isProductive <geneFeature>

Whether specified gene feature will be productive (no stops and is in frame).

-biochemicalProperty <gene_feature> <property>

Biochemical property of specified gene feature normalized by AA sequence size. Possible values: Hydropathy, Charge, Polarity, Volume, Strength, MjEnergy, Kf1, Kf2, Kf3, Kf4, Kf5, Kf6, Kf7, Kf8, Kf9, Kf10, Rim, Surface, Turn, Alpha, Beta, Core, Disorder, N2Strength, N2Hydrophobicity, N2Volume, N2Surface

-baseBiochemicalProperties <gene_feature>

Base biochemical properties of specified gene feature normalized by AA sequence size: N2Strength, N2Hydrophobicity, N2Surface, N2Volume, Charge

Alignment-specific fields

The following fields are only available for exportAlignments:

-readIds

Id(s) of read(s) corresponding to alignment

-descrsR1

Export description lines from initial .fasta or .fastq file for R1 reads (only available if -OsaveOriginalReads= true was used in align command)

-descrsR2

Export description lines from initial .fastq file for R2 reads (only available if -OsaveOriginalReads=true was used in alignn command)

-readHistory

Read history

-cloneId

To which clone alignment was attached (make sure using .clna file as input for exportAlignments)

-cloneIdWithMappingType

To which clone alignment was attached with additional info on mapping type (make sure using .clna file as input for exportAlignments)

Clonotype-specific fields

The following fields are available for exportClones:

-cloneId

Unique clone identifier

-readCount

Number of reads assigned to the clonotype

-readFraction

Fraction of reads assigned to the clonotype

-uniqueTagFraction <(Molecule|Cell|Sample)>

Fraction of unique tags (UMI, CELL, etc.) the clone or alignment collected. Tag type will be used for filtering tags for export.

-cellGroup

Cell group (for single cell analysis)

Default anchor point positions

Positions of anchor points produced by the -defaultAnchorPoints option are outputted as a colon separated list. If an anchor point is not covered by the target sequence nothing is printed for it, but flanking colon symbols are preserved to maintain positions in array. See example:

:::::::::108:117:125:152:186:213:243:244:

If there are several target sequences (e.g. paired-end reads or multi-part clonal sequnce), an array is outputted for each target sequence. In this case arrays are separated by a comma:

2:61:107:107:118:::::::::::::,:::::::::103:112:120:147:181:208:238:239:

Even if there are no anchor points in one of the parts:

:::::::::::::::::,:::::::::108:117:125:152:186:213:243:244:

The following table shows the correspondence between anchor points and positions in the default anchor point array: