Read Pair Orientation
Classify mapped read strands on the same reference after ordering their distinct leftmost alignment starts.
Description
Read-pair orientation depends on both strand directions and which alignment starts farther left.
Read-pair orientation depends on both strand directions and which alignment starts farther left. An inward-facing pair has forward left and reverse right in this convention.
Classify mapped read strands on the same reference after ordering their distinct leftmost alignment starts.
When to use Read Pair Orientation
Use this for the following task: Classify mapped read strands on the same reference after ordering their distinct leftmost alignment starts.
Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
How to use Read Pair Orientation 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 firstReverse, secondReverse, firstPosition, secondPosition using the field table, then run the tool.
- Read leftRightOrientation, inwardFacing. 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 |
|---|---|---|---|
| firstReverse | First reverse | boolean | Required |
| secondReverse | Second reverse | boolean | Required |
| firstPosition | Zero-based leftmost alignment start of a mapped read on the same reference as its mate. | integer; minimum 0 | Required |
| secondPosition | Zero-based leftmost alignment start of the mapped mate; starts must differ. | integer; minimum 0 | Required |
Supply mapped same-reference strand flags and distinct nonnegative leftmost starts. Order by position and report FR, RF, FF or RR.1
leftRightOrientation = ordered F/R letters; inwardFacing = orientation == FR This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| leftRightOrientation | Left right orientation | string |
| inwardFacing | Inward facing | boolean |
{
"input": {
"firstReverse": false,
"secondReverse": true,
"firstPosition": 100,
"secondPosition": 200
},
"output": {
"leftRightOrientation": "FR",
"inwardFacing": true
}
}Limitations and assumptions
Equal starts are rejected. Same-reference mapping, library type and insert-size expectations are caller assumptions.
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 Insert Size QC for this operation: Summarize insert size using mean and sample standard deviation against explicit QC limits.
The implementation reference documents the exact calculation, supported input shapes and returned fields.
References
-
Read Pair Orientation — tool.io
Similar or alternative tools
- SAM Flag Decode
Decode SAM FLAG bits and preserve unsupported high bits explicitly.
- Insert Size QC
Summarize insert size using mean and sample standard deviation against explicit QC limits.