Exon Skipping Psi

Quantify exon-skipping percent-spliced-in from junction counts.

Description

A two-category exon-inclusion share divides inclusion-supporting junction counts by inclusion plus skipping counts.

A two-category exon-inclusion share divides inclusion-supporting junction counts by inclusion plus skipping counts. Counts must already follow the intended junction convention.^[1]

Quantify exon-skipping percent-spliced-in from junction counts.

When to use Exon Skipping Psi

Use this tool to quantify exon-skipping percent-spliced-in from junction counts.

Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.

How to use Exon Skipping Psi and understand its results

Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.
Enter inclusionJunctionReads, skippingJunctionReads, minimumPsiPercent using the field table and calculation rules, then run the tool.
Read psiPercent, skippingPercent, included. The explanation below defines the units, signs, ordering and any flags or placeholder values.
If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.

Input field	Meaning	Value type; see rules below	Requirement
inclusionJunctionReads	Inclusion junction reads	number	Required
skippingJunctionReads	Skipping junction reads	number	Required
minimumPsiPercent	Minimum psi percent	number	Required

Supply nonnegative inclusion/skipping counts with a positive sum and a finite minimum PSI criterion. Return both percentages and an inclusive inclusion flag. No extra adjustment for the number of inclusion junctions is applied.

PSI%=100 inclusion/(inclusion+skipping); skipping%=100−PSI

Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.

Output field	Meaning	Value type
psiPercent	Psi percent	number
skippingPercent	Skipping percent	number
included	Included	boolean

json

{
  "input": {
    "inclusionJunctionReads": 80,
    "skippingJunctionReads": 20,
    "minimumPsiPercent": 50
  },
  "output": {
    "psiPercent": 80,
    "skippingPercent": 20,
    "included": true
  }
}

Limitations and assumptions

The tool does not detect splicing events, normalize junction coverage or test differential splicing. More complex event models can require different denominators.

Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors. A successfully returned false flag is an evaluated outcome; its meaning is explained above.

Alternative or Complementary methods

Use Mutually Exclusive Exon Switch: Identify reciprocal switching between mutually exclusive exons. For a complementary task, use Alternative 3prime Splice Shift: Detect alternative 3-prime acceptor site usage shifts.

References

Exon Skipping Psi — tool.io

Similar or alternative tools

Mutually Exclusive Exon Switch
Identify reciprocal switching between mutually exclusive exons.
Alternative 3prime Splice Shift
Detect alternative 3-prime acceptor site usage shifts.