Effective Transcript Length

Union overlapping exon intervals and subtract fragment length to estimate transcript effective length.

Description

Overlapping exon intervals must be unioned before effective-length calculation.

Overlapping exon intervals must be unioned before effective-length calculation. Half-open intervals count end−start bases, and a fragment-length adjustment can reduce effective length to zero.^[1]

Union overlapping exon intervals and subtract fragment length to estimate transcript effective length.

When to use Effective Transcript Length

Use this tool to union overlapping exon intervals and subtract fragment length to estimate transcript effective length.

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 Effective Transcript Length 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 transcriptLengthBp, exonStartsBp, exonEndsBp, fragmentLengthBp using the field table and calculation rules, then run the tool.
Read exonUnionLengthBp, effectiveLengthBp, overlapBasesBp. 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
transcriptLengthBp	Transcript length bp	integer	Required
exonStartsBp	Exon starts bp	list of number	Required
exonEndsBp	Exon ends bp	list of number	Required
fragmentLengthBp	Fragment length bp	integer	Required

Enter integer transcript/fragment lengths with fragment length at least one, and aligned nonempty exon starts/ends sorted by nondecreasing start. Each interval must satisfy 0≤start<end≤transcriptLength. Merge overlap while accumulating union length, then return union, effective length and duplicated overlap bases. Exon coordinates themselves may be fractional in the runtime.

effectiveLength=max(0,exonUnionLength−fragmentLength+1); overlap=ΣintervalLengths−union

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

Output field	Meaning	Value type
exonUnionLengthBp	Exon union length bp	integer
effectiveLengthBp	Effective length bp	integer
overlapBasesBp	Overlap bases bp	integer

json

{
  "input": {
    "transcriptLengthBp": 500,
    "exonStartsBp": [
      0,
      200,
      300
    ],
    "exonEndsBp": [
      100,
      350,
      400
    ],
    "fragmentLengthBp": 50
  },
  "output": {
    "exonUnionLengthBp": 300,
    "effectiveLengthBp": 251,
    "overlapBasesBp": 50
  }
}

Limitations and assumptions

Coordinates must be on the supplied transcript axis. This single-length approximation does not use a fragment-length distribution or correct bias, and zero effective length needs handling before TPM/FPKM normalization.

Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Lists are limited to 100,000 entries; the rules above may require smaller limits. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.

Alternative or Complementary methods

Use Transcripts Per Million: Normalize transcript length-adjusted abundances to one million TPM. For a complementary task, use Fragments Per Kilobase Million: Calculate fragments per kilobase of transcript per million mapped fragments.

References

Effective Transcript Length — tool.io

Similar or alternative tools

Transcripts Per Million
Normalize transcript length-adjusted abundances to one million TPM.
Fragments Per Kilobase Million
Calculate fragments per kilobase of transcript per million mapped fragments.