Gene Model Junction Support
Validate exon-model introns against coordinate-matched observed junction read evidence.
Description
A transcript’s neighboring exons imply intron coordinates.
A transcript’s neighboring exons imply intron coordinates. Matching observed junction evidence can support these introns under a declared read threshold.
Validate exon-model introns against coordinate-matched observed junction read evidence.
When to use Gene Model Junction Support
Use this for the following task: Validate exon-model introns against coordinate-matched observed junction read evidence.
Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
How to use Gene Model Junction Support 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 exonStarts, exonEnds, junctionStarts, junctionEnds, junctionReadCounts, minimumReadCount using the field table, then run the tool.
- Read supportedIntronCount, intronCount, supportedFraction. 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 |
|---|---|---|---|
| exonStarts | Exon starts | list of integer; minimum entries 2; maximum entries 100000; each entry: integer; minimum 0 | Required |
| exonEnds | Exon ends | list of integer; minimum entries 2; maximum entries 100000; each entry: integer; minimum 0 | Required |
| junctionStarts | Zero-based inclusive intron starts, matching the preceding exon end. | list of integer; minimum entries 0; maximum entries 100000; each entry: integer; minimum 0 | Required |
| junctionEnds | Zero-based exclusive intron ends, matching the following exon start. | list of integer; minimum entries 0; maximum entries 100000; each entry: integer; minimum 0 | Required |
| junctionReadCounts | Junction read counts | list of integer; minimum entries 0; maximum entries 100000; each entry: integer; minimum 0 | Required |
| minimumReadCount | Minimum read count | integer; minimum 1 | Required |
Supply ordered separated half-open exons and aligned positive-length junctions. Combine counts for identical junctions only up to the support threshold, then report supported introns and fraction.1
intron i = [exonEnd[i−1],exonStart[i]); supported if matched read count ≥ minimum This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| supportedIntronCount | Supported intron count | integer |
| intronCount | Intron count | integer |
| supportedFraction | Supported fraction | number |
{
"input": {
"exonStarts": [
0,
20,
40
],
"exonEnds": [
10,
30,
50
],
"junctionStarts": [
10,
30
],
"junctionEnds": [
20,
40
],
"junctionReadCounts": [
8,
1
],
"minimumReadCount": 3
},
"output": {
"supportedIntronCount": 1,
"intronCount": 2,
"supportedFraction": 0.5
}
}Limitations and assumptions
Coordinates must already share a reference and convention. The tool does not align RNA reads or establish expression of a full transcript.
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 CIGAR Junction Positions for this operation: Extract zero-based half-open reference skip junctions from CIGAR N operations. For a complementary task, use Cassette Junction Evidence for this operation: Require both cassette inclusion junctions and a direct skipping junction as event evidence.
The implementation reference documents the exact calculation, supported input shapes and returned fields.
References
-
Gene Model Junction Support — tool.io
Similar or alternative tools
- CIGAR Junction Positions
Extract zero-based half-open reference skip junctions from CIGAR N operations.
- Cassette Junction Evidence
Require both cassette inclusion junctions and a direct skipping junction as event evidence.