cmuts div¶

Purpose¶

Normalization of reactivity rates against a denatured control.

Requires¶

Reactivity rates, usually the output of cmuts sub
Denatured control reactivity rates

Both must be in cmuts-compatible HDF5 files.

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. The result is NaN if either input is NaN there, or if the control’s rate is not above zero.

Error and Coverage¶

The error is computed via the standard propagation of error for a ratio. The coverage and the four read-related datasets simply take the sum of the treated and untreated values.

Warning

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

Output¶

`coverage`¶

Shape (n, l) · Type float32 · Fill zero

The number of reads in which this base was present.

`reactivity`¶

Shape (n, l) · Type float32 · Fill NaN

The mutation rate of the sample divided by that of the control, so a position reads as its rate relative to the denatured state.

`error`¶

Shape (n, l) · Type float32 · Fill NaN

Standard error of the reactivity values. Purely the statistical error introduced by finite read depths; does not account for experimental or systemic errors.

`reads/lengths`¶

Shape (n, 2l) · Type uint64 · Fill zero

The number of reads passing all filters, binned by length.

`reads/counted`¶

Shape (n,) · Type uint64 · Fill zero

The number of reads passing all filters.

`reads/rejected`¶

Shape (n,) · Type uint64 · Fill zero

The number of reads rejected by at least one filter, or which couldn’t be modelled by the HMM

`reads/unmapped`¶

Shape () · Type uint64 · Fill zero

The number of reads not aligned to any reference.

CLI Options¶

Arguments¶

Argument	Description
`RATES`	the reactivities to normalize
`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