RNA Editing Frequency

Calculate A-to-I RNA-editing frequency from aligned read counts.

Description

An editing frequency is the edited share of reads covering a site.

An editing frequency is the edited share of reads covering a site. A caller threshold can classify that share without identifying the molecular cause of mismatches.^[1]

Calculate A-to-I RNA-editing frequency from aligned read counts.

When to use RNA Editing Frequency

Use this tool to calculate A-to-I RNA-editing frequency from aligned read counts.

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 RNA Editing Frequency 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 editedReads, totalCoveredReads, minimumEditingPercent using the field table and calculation rules, then run the tool.
Read editingPercent, uneditedReads, edited. 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
editedReads	Edited reads	number	Required
totalCoveredReads	Total covered reads	number	Required
minimumEditingPercent	Minimum editing percent	number	Required

Supply positive coverage, nonnegative edited reads not exceeding coverage and a finite minimum percentage. Return editing percentage, remaining unedited count and an inclusive threshold flag.

editing%=100 editedReads/coverage; unedited=coverage−editedReads

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

Output field	Meaning	Value type
editingPercent	Editing percent	number
uneditedReads	Unedited reads	number
edited	Edited	boolean

json

{
  "input": {
    "editedReads": 15,
    "totalCoveredReads": 100,
    "minimumEditingPercent": 10
  },
  "output": {
    "editingPercent": 15,
    "uneditedReads": 85,
    "edited": true
  }
}

Limitations and assumptions

The tool does not align reads or distinguish A-to-I editing from variants, errors or contamination. A threshold label is not a biological or clinical confirmation.

Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. 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 Multimapper Fraction: Measure ambiguous multi-mapper assignment share. For a complementary task, use RRNA Contamination: Flag rRNA contamination in a sequenced RNA library.

References

RNA Editing Frequency — tool.io

Similar or alternative tools

Multimapper Fraction
Measure ambiguous multi-mapper assignment share.
RRNA Contamination
Flag rRNA contamination in a sequenced RNA library.