cmuts sub

Purpose

Background subtraction of mismatch, insertion, deletion, and termination rates.

Requires

• A treated sample

• An untreated sample

Each must be a cmuts-compatible HDF5 file holding at least one of the four rates that cmuts works with.

Usage

cmuts sub -o difference.h5 treated.h5 untreated.h5

Each untreated rate is subtracted from its treated counterpart when both are present. The result is NaN if either input is NaN there. A negative difference is raised to zero, unless --keep-negative is given.

Note

Subtraction and clipping is the maximum likelihood estimator for non-negative treatment-mediated rates under a mixture model.

If any dataset does not match the expected shape or the stored sequences do not match, the program exits early.

Output

Dataset	Source
mismatches/rate	Treated less untreated.
mismatches/error	Propagated from the inputs.
insertions/rate	Treated less untreated.
insertions/error	Propagated from the inputs.
deletions/rate	Treated less untreated.
deletions/error	Propagated from the inputs.
terminations/rate	Treated less untreated.
terminations/error	Propagated from the inputs.
coverage	Summed over the inputs.
sequence	Copied from the inputs.
reads/length-histogram	Summed over the inputs.
reads/quality-histogram	Summed over the inputs.
reads/primary/counted	Summed over the inputs.
reads/primary/rejected	Summed over the inputs.
reads/supplementary/counted	Summed over the inputs.
reads/supplementary/rejected	Summed over the inputs.
reads/unmapped	Summed over the inputs.

Warning

High coverage in the output does not imply high-quality data, since it is insensitive to imbalances in the treated and untreated experiments. Either ensure each experiment separately has high coverage or use the signal-to-noise ratio as a more robust quality metric.

CLI Options

Arguments

Argument	Description
TREATED	the treated sample
UNTREATED	the untreated background

Input and output

Option	Description
-o, --output HDF5	write results to this file (required)
--overwrite	replace the output file if it already exists

Subtraction

Option	Description
--keep-negative	do not clip negative values after subtraction

Information

Option	Description
-h, --help	show this help and exit
-V, --version	show the version and exit

Advanced

Accepted, and left out of --help.

Option	Description
--dump-options	describe every argument as JSON and exit
--dump-layout	describe the output format as JSON and exit