Length Normalized PSI
Quantify PSI from inclusion and skipping counts normalized by their effective lengths.
Description
Percent spliced in compares inclusion with skipping evidence.
Percent spliced in compares inclusion with skipping evidence. Effective-length normalization adjusts counts for their different observation opportunities.
Quantify PSI from inclusion and skipping counts normalized by their effective lengths.
When to use Length Normalized PSI
Use this for the following task: Quantify PSI from inclusion and skipping counts normalized by their effective lengths.
Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
How to use Length Normalized PSI 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 inclusionReads, skippingReads, inclusionEffectiveLength, skippingEffectiveLength using the field table, then run the tool.
- Read inclusionDensity, skippingDensity, psiPercent. 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 |
|---|---|---|---|
| inclusionReads | Inclusion reads | integer; minimum 0 | Required |
| skippingReads | Skipping reads | integer; minimum 0 | Required |
| inclusionEffectiveLength | Inclusion effective length | number; greater than 0 | Required |
| skippingEffectiveLength | Skipping effective length | number; greater than 0 | Required |
Supply nonnegative counts, positive effective lengths and at least one positive density. Normalize and use scaled arithmetic when needed to avoid overflow.1
inclusionDensity = inclusionReads/inclusionLength; PSI% = 100 inclusionDensity/(inclusionDensity+skippingDensity) This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| inclusionDensity | Inclusion density | number |
| skippingDensity | Skipping density | number |
| psiPercent | Psi percent | number |
{
"input": {
"inclusionReads": 80,
"skippingReads": 20,
"inclusionEffectiveLength": 200,
"skippingEffectiveLength": 100
},
"output": {
"inclusionDensity": 0.4,
"skippingDensity": 0.2,
"psiPercent": 66.66666666666666
}
}Limitations and assumptions
This does not estimate effective lengths, resolve isoforms or provide statistical uncertainty.
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 Cassette Junction Evidence for this operation: Require both cassette inclusion junctions and a direct skipping junction as event evidence. For a complementary task, use Intron Coverage Boundary for this operation: Compare intron coverage with flanking exon depth to screen retention evidence.
The implementation reference documents the exact calculation, supported input shapes and returned fields.
References
-
Length Normalized PSI — tool.io
Similar or alternative tools
- Cassette Junction Evidence
Require both cassette inclusion junctions and a direct skipping junction as event evidence.
- Intron Coverage Boundary
Compare intron coverage with flanking exon depth to screen retention evidence.