Multimapper Fraction
Measure ambiguous multi-mapper assignment share.
Description
Ambiguously mapped reads share assignment across possible locations.
Ambiguously mapped reads share assignment across possible locations. Their supplied fraction measures assignment ambiguity rather than independently identifying multimapping alignments.1
Measure ambiguous multi-mapper assignment share.
When to use Multimapper Fraction
Use this tool to measure ambiguous multi-mapper assignment share.
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 Multimapper Fraction 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 ambiguousReads, mappedReads, maximumAmbiguousPercent using the field table and calculation rules, then run the tool.
- Read ambiguousPercent, uniqueReads, passes. 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 |
|---|---|---|---|
| ambiguousReads | Ambiguous reads | number | Required |
| mappedReads | Mapped reads | number | Required |
| maximumAmbiguousPercent | Maximum ambiguous percent | number | Required |
Enter a positive mapped total and nonnegative ambiguous reads no larger than it, with a finite maximum criterion. Return ambiguous percentage, remaining unique count and an inclusive percentage≤maximum pass flag.
ambiguous%=100 ambiguousReads/mappedReads; unique=mapped−ambiguous Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| ambiguousPercent | Ambiguous percent | number |
| uniqueReads | Unique reads | number |
| passes | Passes | boolean |
{
"input": {
"ambiguousReads": 20,
"mappedReads": 100,
"maximumAmbiguousPercent": 10
},
"output": {
"ambiguousPercent": 20,
"uniqueReads": 80,
"passes": false
}
}Limitations and assumptions
No alignment or reassignment is performed. Read and fragment counting conventions must match; fractional values and percentage criteria 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 Complexity: Measure duplicate fraction and library complexity from distinct fragments. For a complementary task, use RRNA Contamination: Flag rRNA contamination in a sequenced RNA library.
References
-
Multimapper Fraction — tool.io
Similar or alternative tools
- Library Complexity
Measure duplicate fraction and library complexity from distinct fragments.
- RRNA Contamination
Flag rRNA contamination in a sequenced RNA library.