Gene Body Coverage Bias

Detect 3-prime RNA coverage bias from aggregated end-of-gene read depth.

Description

A 3′-to-5′ aggregate coverage ratio describes directional gene-body bias.

A 3′-to-5′ aggregate coverage ratio describes directional gene-body bias. Positive log2 values favor the 3′ end, while negative values favor the 5′ end.^[1]

Detect 3-prime RNA coverage bias from aggregated end-of-gene read depth.

When to use Gene Body Coverage Bias

Use this tool to detect 3-prime RNA coverage bias from aggregated end-of-gene read depth.

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 Bias 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 fivePrimeReadCounts, threePrimeReadCounts, maximumAbsoluteLog2Bias using the field table and calculation rules, then run the tool.
Read fivePrimeTotal, threePrimeTotal, log2ThreeToFiveBias, degraded. 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
fivePrimeReadCounts	Five prime read counts	list of number	Required
threePrimeReadCounts	Three prime read counts	list of number	Required
maximumAbsoluteLog2Bias	Maximum absolute log 2 bias	number	Required

Enter two nonempty finite coverage lists with positive sums and a finite criterion. Their lengths need not match. Sum each end, take the log2 ratio and return totals, signed bias and the inclusive flag. Despite maximumAbsoluteLog2Bias in the input name, the comparison uses signed bias without absolute value.

bias=log2(sumThreePrime/sumFivePrime); degraded=(bias≥criterion)

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

Output field	Meaning	Value type
fivePrimeTotal	Five prime total	number
threePrimeTotal	Three prime total	number
log2ThreeToFiveBias	Log 2 three to five bias	number
degraded	Degraded	boolean

json

{
  "input": {
    "fivePrimeReadCounts": [
      10,
      10
    ],
    "threePrimeReadCounts": [
      20,
      20
    ],
    "maximumAbsoluteLog2Bias": 0.5
  },
  "output": {
    "fivePrimeTotal": 20,
    "threePrimeTotal": 40,
    "log2ThreeToFiveBias": 1,
    "degraded": true
  }
}

Limitations and assumptions

Individual negative entries are not separately rejected when totals are positive. The flag does not prove RNA degradation, and coverage normalization, annotation and sampling uncertainty are excluded.

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 Uniformity: Rate gene-body coverage uniformity using decile coefficient of variation. For a complementary task, use DV200 Fragment Quality: Calculate the share of RNA fragments longer than a user-selected cutoff.

References

Gene Body Coverage Bias — tool.io

Similar or alternative tools

Gene Body Coverage Uniformity
Rate gene-body coverage uniformity using decile coefficient of variation.
DV200 Fragment Quality
Calculate the share of RNA fragments longer than a user-selected cutoff.