Marked Duplicate Fraction
Compute marked-duplicate read fraction without assuming unmarked reads are unique molecules.
Description
Duplicate marking labels selected reads according to an upstream algorithm.
Duplicate marking labels selected reads according to an upstream algorithm. Unmarked reads should not automatically be equated with independent molecules.
Compute marked-duplicate read fraction without assuming unmarked reads are unique molecules.
When to use Marked Duplicate Fraction
Use this for the following task: Compute marked-duplicate read fraction without assuming unmarked reads are unique molecules.
Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
How to use Marked Duplicate Fraction 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 markedDuplicates, totalReads using the field table, then run the tool.
- Read duplicatePercent, unmarkedReadCount. 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 |
|---|---|---|---|
| markedDuplicates | Marked duplicates | integer; minimum 0 | Required |
| totalReads | Total reads | integer; minimum 1 | Required |
Supply nonnegative marked count no greater than a positive total. Return the fraction as percent and the remainder.1
duplicatePercent = 100 markedDuplicates/totalReads; unmarked = total − marked This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| duplicatePercent | Duplicate percent | number |
| unmarkedReadCount | Unmarked read count | integer |
{
"input": {
"markedDuplicates": 20,
"totalReads": 100
},
"output": {
"duplicatePercent": 20,
"unmarkedReadCount": 80
}
}Limitations and assumptions
No duplicates are marked here. UMI handling, optical duplicates and molecule counts require upstream processing.
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 SAM Flag Decode for this operation: Decode SAM FLAG bits and preserve unsupported high bits explicitly. For a complementary task, use Overrepresented Read Screen for this operation: Flag exact-sequence read abundance fractions above a caller-defined overrepresentation ceiling.
The implementation reference documents the exact calculation, supported input shapes and returned fields.
References
-
Marked Duplicate Fraction — tool.io
Similar or alternative tools
- SAM Flag Decode
Decode SAM FLAG bits and preserve unsupported high bits explicitly.
- Overrepresented Read Screen
Flag exact-sequence read abundance fractions above a caller-defined overrepresentation ceiling.