`mixcr exportQc`

Exports various quality control metrics in a graphical form. Supported file formats: PDF, EPS, SVG, PNG and JPEG.

Alignment reports

mixcr exportQc align
    [--absolute-values] 
    [--width <n> --height <n>] 
    [--force-overwrite] 
    [--no-warnings] 
    [--verbose] 
    [--help] 
    sample.(vdjca|clns|clna)... align.(pdf|eps|svg|png|jpeg)

Exports alignment reports.

sample.(vdjca|clns|clna)...: Paths to input files with alignments
align.(pdf|eps|svg|png|jpeg): Path where to write output plots
--absolute-values: Plot in absolute values instead of percent
--width <n>: Plot width
--height <n>: Plot height
-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.

Example:

mixcr exportQc align *.vdjca alignQc.pdf

Reads coverage

mixcr exportQc coverage
    [--show-boundaries] 
    [--force-overwrite] 
    [--no-warnings] 
    [--verbose] 
    [--help] 
    sample.vdjca... coverage.(pdf|eps|svg|png|jpeg)

Exports anchor points coverage by the library. It separately plots coverage for R1, R2 and overlapping reads.

sample.vdjca...: Paths to input files
coverage.(pdf|eps|svg|png|jpeg): Path where to write output plots
--show-boundaries: Show V alignment begin and J alignment end
-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.

Example:

mixcr exportQc coverage SRR18293077.vdjca coverage.pdf

R1R2Overlap

Chain usage

mixcr exportQc chainUsage
    [--absolute-values] 
    [--align-chain-usage] 
    [--hide-non-functional] 
    [--width <n> --height <n>] 
    [--force-overwrite] 
    [--no-warnings] 
    [--verbose] 
    [--help] 
    sample.(vdjca|clns|clna)... usage.(pdf|eps|svg|png|jpeg)

Exports chain usage summary in either alignments (.vdjca) or clonotypes (.clns).

Command line options are:

sample.(vdjca|clns|clna)...: Paths to input files
usage.(pdf|eps|svg|png|jpeg): Path where to write output plots
--absolute-values: Plot in absolute values instead of percent
--align-chain-usage: When specifying .clnx files on input force to plot chain usage for alignments
--hide-non-functional: Hide fractions of non-functional CDR3s (out-of-frames and containing stops)
--width <n>: Plot width
--height <n>: Plot height
-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.

Example:

> mixcr exportQc chainUsage --hide-non-functional results/*.clns chainUsage.pdf

Barcodes

mixcr exportQc tags 
    [--log] 
    [--force-overwrite] 
    [--no-warnings] 
    [--verbose] 
    [--help]
    sample.(vdjca|clns|clna)... coverage.(pdf|eps|svg|png|jpeg)

Tag refinement statistics plots.

sample.(vdjca|clns|clna)...: Paths to input files
coverage.(pdf|eps|svg|png|jpeg): Path where to write output plots
--log: Use log10 scale for y-axis
-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.

For example, for 10x VDJ data:

> mixcr exportQc tags 10x-data.clns barcodesFiltering.pdf

The upper plot shows reads per UMI distribution and cut-off threshold used to filter erroneous UMIs. The second plot shows UMI per cell barcode distribution and cut-off threshold used to filter erroneous cell barcodes.