RRNA Contamination

Flag rRNA contamination in a sequenced RNA library.

Description

The rRNA share measures how much mapped-read coverage is assigned to ribosomal RNA.

The rRNA share measures how much mapped-read coverage is assigned to ribosomal RNA. Its denominator must match the caller's read-counting convention.^[1]

Flag rRNA contamination in a sequenced RNA library.

When to use RRNA Contamination

Use this tool to flag rRNA contamination in a sequenced RNA library.

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 RRNA Contamination 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 rrnaAlignedReads, mappedReads, maximumRrnaPercent using the field table and calculation rules, then run the tool.
Read rrnaPercent, contaminationFlag. 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
rrnaAlignedReads	rRNA aligned reads	number	Required
mappedReads	Mapped reads	number	Required
maximumRrnaPercent	Maximum rrna percent	number	Required

Supply a positive mapped total, nonnegative rRNA reads no larger than that total and a finite maximum percentage. Return rRNA percentage and a strictly-above contamination flag, so equality does not flag.

rRNA%=100 rRNAaligned/mapped; flag=rRNA%>maximum

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

Output field	Meaning	Value type
rrnaPercent	rRNA percent	number
contaminationFlag	Contamination flag	boolean

json

{
  "input": {
    "rrnaAlignedReads": 8,
    "mappedReads": 100,
    "maximumRrnaPercent": 5
  },
  "output": {
    "rrnaPercent": 8,
    "contaminationFlag": true
  }
}

Limitations and assumptions

No rRNA alignment or classification is performed. The criterion is supplied rather than an embedded QC recommendation, and fractional counts/thresholds outside 0–100 are not separately rejected.

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 Library Mito Fraction: Screen a bulk RNA library for elevated mitochondrial-read fraction. For a complementary task, use Multimapper Fraction: Measure ambiguous multi-mapper assignment share.

References

RRNA Contamination — tool.io

Similar or alternative tools

Library Mito Fraction
Screen a bulk RNA library for elevated mitochondrial-read fraction.
Multimapper Fraction
Measure ambiguous multi-mapper assignment share.