mixcr extend

Imputes germline sequences to the uncovered edges of CDR3, if corresponding V or J gene for is uniquely determined (e.g. from the second mate of a read pair).

This procedure is typically used as a part of non-targeted RNA-Seq analysis pipeline for T-cells, to recover some of useful TCRs. It is not safe to use it for IGs, because of hypermutations. Tor TCRs which have relatively conservative sequence near conserved Cys and Phe/Trp, it can reconstruct additional clonotypes with relatively small chance to introduce false ones. Default parameters are specifically optimized to show zero false-positive rate. By default mixcr extend acts only on TCR sequences.

Command line options

mixcr extend [--v-anchor <anchor_point>] [--j-anchor <anchor_point>] [--min-v-score <n>] [--min-j-score <n>] [--chains <chains>] [--quality <n>] [--report <path>] [--json-report <path>] [--threads <n>] [--force-overwrite] [--no-warnings] [--verbose] [--help] data.(vdjca|clns|clna) extendeed.(vdjca|clns|clna)

The command takes alignments (.vdjca) or clones (.clnx) file as input and produces the same format as output. Additionally, it produces a comprehensive report.

Basic command line options are:

data.(vdjca|clns|clna)

Path to input file.

extendeed.(vdjca|clns|clna)

Path where to write output. Will have the same file type.

--v-anchor <anchor_point>

V extension anchor point. Default value determined by the preset.

--j-anchor <anchor_point>

J extension anchor point. Default value determined by the preset.

--min-v-score <n>

Minimal V hit score to perform left extension. Default value determined by the preset.

--min-j-score <n>

Minimal J hit score to perform right extension. Default value determined by the preset.

-c, --chains <chains>

Apply procedure only to alignments with specific immunological-receptor chains. Default: TCR

-q, --quality <n>

Quality score value to assign imputed sequences. Default: 30

-r, --report <path>

Report file (human readable version, see -j / --json-report for machine readable report).

-j, --json-report <path>

JSON formatted report file.

-t, --threads <n>

Processing threads

-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.