Overrepresented Read Screen
Flag exact-sequence read abundance fractions above a caller-defined overrepresentation ceiling.
Description
Repeated exact read sequences can be overrepresented relative to a library.
Repeated exact read sequences can be overrepresented relative to a library. Their abundance fractions provide one focused quality-control screen.
Flag exact-sequence read abundance fractions above a caller-defined overrepresentation ceiling.
When to use Overrepresented Read Screen
Use this for the following task: Flag exact-sequence read abundance fractions above a caller-defined overrepresentation ceiling.
Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
How to use Overrepresented Read Screen and understand its results
- Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
- Enter sequenceCounts, totalReads, maximumFraction using the field table, then run the tool.
- Read sequenceFractions, flaggedIndexes. Interpret flags, units, ordering and placeholder values using the rules below.
- Review any reported issue or failed check, correct the supplied values when appropriate, and verify the result in its intended context.
| Input field | Meaning | Value type and bounds | Requirement |
|---|---|---|---|
| sequenceCounts | Counts of distinct exact sequences among totalReads; the sum cannot exceed totalReads. | list of integer; minimum entries 1; maximum entries 100000; each entry: integer; minimum 0 | Required |
| totalReads | Total reads | integer; minimum 1 | Required |
| maximumFraction | Maximum fraction | number; minimum 0; maximum 1 | Required |
Use nonnegative distinct-sequence counts totaling no more than positive total reads. Compare with the supplied fraction ceiling and return zero-based flagged indices.1
fraction[i] = sequenceCount[i]/totalReads; flag if fraction > maximumFraction This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| sequenceFractions | Sequence fractions | list of number |
| flaggedIndexes | Flagged indexes | list of integer |
{
"input": {
"sequenceCounts": [
10,
40
],
"totalReads": 100,
"maximumFraction": 0.2
},
"output": {
"sequenceFractions": [
0.1,
0.4
],
"flaggedIndexes": [
1
]
}
}Limitations and assumptions
Equality is not flagged. The tool does not identify sequences, assign contamination sources or distinguish biological abundance from technical duplication.
The tool operates on supplied local data; alignment, filtering and annotation must already be appropriate for the stated calculation. Malformed requests produce input errors. A successfully evaluated request can still contain false flags, empty result lists or a result outside the supplied threshold; those outcomes have the meanings stated above.
Alternative or Complementary methods
Choose Trailing Adapter Contamination for this operation: Detect read-terminal matches to an adapter prefix above the chosen minimum match length. For a complementary task, use Marked Duplicate Fraction for this operation: Compute marked-duplicate read fraction without assuming unmarked reads are unique molecules.
The implementation reference documents the exact calculation, supported input shapes and returned fields.
References
-
Overrepresented Read Screen — tool.io
Similar or alternative tools
- Trailing Adapter Contamination
Detect read-terminal matches to an adapter prefix above the chosen minimum match length.
- Marked Duplicate Fraction
Compute marked-duplicate read fraction without assuming unmarked reads are unique molecules.