cmuts norm¶

Purpose¶

Experiment-independent normalization of reactivity rates.

Requires¶

One or more sets of reactivity rates, in cmuts-compatible HDF5 files

Usage¶

Every input given to one run shares a single norm, and each is written to an output of its own. --output is repeated once per input and paired with them in order.

cmuts norm -o apo-normalized.h5 -o holo-normalized.h5 apo.h5 holo.h5

Running the inputs separately gives each its own norm instead.

cmuts norm -o apo-normalized.h5 apo.h5
cmuts norm -o holo-normlized.h5 holo.h5

Pool the inputs whenever the rates are to be compared across experiments, since a norm of its own puts each experiment on a different footing.

Normalization Schemes¶

--norm ubr (the default) takes the 90th percentile of the pooled rates, counting only positions whose coverage exceeds --min-coverage. --norm outlier drops the highest 2% of the pooled rates as outliers and averages what lies between there and the highest 10%; it reads no coverage, so --min-coverage does not apply to it.

A norm that comes out as zero, negative, or undefined is not applied and is recorded as NaN.

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 divided by the norm this file records, so a rate reads against the norm rather than as a raw frequency.

`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.

`norm`¶

Shape () · Type float32 · Fill NaN

The norm every rate in this file was divided by.

CLI Options¶

Arguments¶

Argument	Description
`RATES...`	the reactivities to normalize

Input and output¶

Option	Description
`-o, --output HDF5`	write one input’s results to this file; repeat once per input (required)
`--overwrite`	replace the output files if they already exist

Normalization¶

Option	Description
`--norm SCHEME`	how the norm is taken from the rates (ubr, outlier; default ubr)
`--min-coverage N`	coverage a position needs before its rate sets the norm (ubr only) (default 500)

Clipping¶

Option	Description
`--clip-above N`	lower a normalized reactivity down to this value (default: none)

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