cmuts div

Purpose

Normalization of mismatch, insertion, deletion, and termination rates against a denatured control.

Requires

• A sample to normalize, usually the output of cmuts sub

• A denatured control sample

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

Usage

The control is applied after the background is subtracted.

cmuts sub -o difference.h5 treated.h5 untreated.h5
cmuts div -o normalized.h5 difference.h5 denatured.h5

Each rate is divided by the control’s rate at the same position when both are present. The result is NaN if either input is NaN there, or if the control’s rate is not above zero.

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

Output

Dataset	Source
mismatches/rate	Sample over control.
mismatches/error	Propagated from the inputs.
insertions/rate	Sample over control.
insertions/error	Propagated from the inputs.
deletions/rate	Sample over control.
deletions/error	Propagated from the inputs.
terminations/rate	Sample over control.
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.

CLI Options

Arguments

Argument	Description
RATES	the reactivities to divide
CONTROL	the denatured control

Input and output

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

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