Gene Body Coverage Uniformity

Rate gene-body coverage uniformity using decile coefficient of variation.

Description

Coverage uniformity can be summarized by a population CV across gene-body bins.

Coverage uniformity can be summarized by a population CV across gene-body bins. Equal bins with identical coverage give zero variation.^[1]

Rate gene-body coverage uniformity using decile coefficient of variation.

When to use Gene Body Coverage Uniformity

Use this tool to rate gene-body coverage uniformity using decile coefficient of variation.

Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.

How to use Gene Body Coverage Uniformity and understand its results

Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.
Enter decileReadCounts, maximumCvPercent using the field table and calculation rules, then run the tool.
Read meanDecileReads, coefficientOfVariationPercent, uniform. The explanation below defines the units, signs, ordering and any flags or placeholder values.
If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.

Input field	Meaning	Value type; see rules below	Requirement
decileReadCounts	Decile read counts	list of number	Required
maximumCvPercent	Maximum cv percent	number	Required

Enter at least two nonnegative coverage bins with positive mean and a finite maximum CV criterion. Compute mean and population SD, then return CV and an inclusive uniformity flag. The name says decile, but the calculator does not require exactly ten bins.

CV%=100 populationSD(binCounts)/mean(binCounts)

Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.

Output field	Meaning	Value type
meanDecileReads	Mean decile reads	number
coefficientOfVariationPercent	Coefficient of variation percent	number
uniform	Uniform	boolean

json

{
  "input": {
    "decileReadCounts": [
      10,
      10,
      10,
      10
    ],
    "maximumCvPercent": 5
  },
  "output": {
    "meanDecileReads": 10,
    "coefficientOfVariationPercent": 0,
    "uniform": true
  }
}

Limitations and assumptions

Bins should use comparable widths and aggregation conventions. No alignments or gene-body profiles are generated, and the flag cannot distinguish biological coverage patterns from technical bias.

Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Lists are limited to 100,000 entries; the rules above may require smaller limits. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors. A successfully returned false flag is an evaluated outcome; its meaning is explained above.

Alternative or Complementary methods

Use Gene Body Coverage Bias: Detect 3-prime RNA coverage bias from aggregated end-of-gene read depth. For a complementary task, use Housekeeping Cv Rank: Rank housekeeping genes by replicate coefficient of variation.

References

Gene Body Coverage Uniformity — tool.io

Similar or alternative tools

Gene Body Coverage Bias
Detect 3-prime RNA coverage bias from aggregated end-of-gene read depth.
Housekeeping Cv Rank
Rank housekeeping genes by replicate coefficient of variation.