cmuts sub¶

Purpose¶

Background subtraction of reactivity rates.

Requires¶

Treated reactivity rates
Untreated reactivity rates

Both must be in cmuts-compatible HDF5 files.

Error and Coverage¶

The error of the background-subtracted rates is computed using the standard quadrature formula. The coverage and the four read-related datasets simply take the sum of the treated and untreated values.

To normalize the result against a denatured control, pass it to cmuts div.

Warning

High coverage in the output dataset 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.

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 treated sample less that of the untreated one, so what remains is the signal the treatment added.

`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
`TREATED`	the modified sample
`UNTREATED`	the 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
`--clip`	raise a negative reactivity to zero

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