Cassette Junction Evidence
Require both cassette inclusion junctions and a direct skipping junction as event evidence.
Description
A cassette exon event can have inclusion junctions on both sides and a direct skipping junction.
A cassette exon event can have inclusion junctions on both sides and a direct skipping junction. Requiring all three types avoids using one inclusion edge alone.
Require both cassette inclusion junctions and a direct skipping junction as event evidence.
When to use Cassette Junction Evidence
Use this for the following task: Require both cassette inclusion junctions and a direct skipping junction as event 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 Cassette Junction Evidence 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 upstreamInclusionReads, downstreamInclusionReads, skippingReads, minimumJunctionReads using the field table, then run the tool.
- Read inclusionPairSupported, skippingSupported, cassetteEventSupported. 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 |
|---|---|---|---|
| upstreamInclusionReads | Upstream inclusion reads | integer; minimum 0 | Required |
| downstreamInclusionReads | Downstream inclusion reads | integer; minimum 0 | Required |
| skippingReads | Skipping reads | integer; minimum 0 | Required |
| minimumJunctionReads | Minimum junction reads | integer; minimum 1 | Required |
Supply nonnegative counts and a positive support threshold. Check both inclusion counts and the skipping count inclusively.1
inclusionPair = min(leftReads,rightReads) ≥ minimum; event = inclusionPair AND skippingSupported This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| inclusionPairSupported | Inclusion pair supported | boolean |
| skippingSupported | Skipping supported | boolean |
| cassetteEventSupported | Cassette event supported | boolean |
{
"input": {
"upstreamInclusionReads": 10,
"downstreamInclusionReads": 8,
"skippingReads": 5,
"minimumJunctionReads": 3
},
"output": {
"inclusionPairSupported": true,
"skippingSupported": true,
"cassetteEventSupported": true
}
}Limitations and assumptions
This is caller-supplied count evidence, not a splice-event caller or statistical differential-splicing test.
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 Length Normalized PSI for this operation: Quantify PSI from inclusion and skipping counts normalized by their effective lengths. For a complementary task, use Gene Model Junction Support for this operation: Validate exon-model introns against coordinate-matched observed junction read evidence.
The implementation reference documents the exact calculation, supported input shapes and returned fields.
References
-
Cassette Junction Evidence — tool.io
Similar or alternative tools
- Length Normalized PSI
Quantify PSI from inclusion and skipping counts normalized by their effective lengths.
- Gene Model Junction Support
Validate exon-model introns against coordinate-matched observed junction read evidence.