Intron Coverage Boundary
Compare intron coverage with flanking exon depth to screen retention evidence.
Description
Intron coverage relative to flanking exon coverage can provide retention evidence.
Intron coverage relative to flanking exon coverage can provide retention evidence. Coverage alone does not identify the complete transcript structure.
Compare intron coverage with flanking exon depth to screen retention evidence.
When to use Intron Coverage Boundary
Use this for the following task: Compare intron coverage with flanking exon depth to screen retention 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 Intron Coverage Boundary 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 upstreamExonDepth, intronDepth, downstreamExonDepth, minimumIntronExonRatio using the field table, then run the tool.
- Read intronExonRatio, leftDropFraction, rightRiseFraction, retentionCandidate. 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 |
|---|---|---|---|
| upstreamExonDepth | Upstream exon depth | number; greater than 0 | Required |
| intronDepth | Intron depth | number; minimum 0 | Required |
| downstreamExonDepth | Downstream exon depth | number; greater than 0 | Required |
| minimumIntronExonRatio | Minimum intron exon ratio | number; minimum 0; maximum 1 | Required |
Use positive flanking depths and supported nonnegative intron depth. Return normalized ratios and test retention when the intron/exon ratio meets the caller threshold inclusively.1
ratio = intronDepth/mean(flankDepths); boundary fractions = 1−intronDepth/flankDepth This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| intronExonRatio | Intron exon ratio | number |
| leftDropFraction | Left drop fraction | number |
| rightRiseFraction | Right rise fraction | number |
| retentionCandidate | Retention candidate | boolean |
{
"input": {
"upstreamExonDepth": 20,
"intronDepth": 10,
"downstreamExonDepth": 20,
"minimumIntronExonRatio": 0.4
},
"output": {
"intronExonRatio": 0.5,
"leftDropFraction": 0.5,
"rightRiseFraction": 0.5,
"retentionCandidate": true
}
}Limitations and assumptions
Boundary fractions can be negative if intron coverage exceeds a flank. This is a candidate screen rather than proof of retained introns.
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
-
Intron Coverage Boundary — 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.