Junction Annotation Tally

Tally annotated versus novel observed splice junctions.

Description

Junction annotation matching compares observed identifiers with a supplied reference list.

Junction annotation matching compares observed identifiers with a supplied reference list. Exact-string matching requires consistent coordinate, strand and naming conventions upstream.^[1]

Tally annotated versus novel observed splice junctions.

When to use Junction Annotation Tally

Use this tool to tally annotated versus novel observed splice junctions.

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 Junction Annotation Tally 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 observedJunctionIds, annotatedJunctionIds using the field table and calculation rules, then run the tool.
Read annotatedCount, novelCount, novelJunctionIds. 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
observedJunctionIds	Observed junction ids	list of string	Required
annotatedJunctionIds	Annotated junction ids	list of string	Required

Enter a nonempty observed ID list and an annotation list, which may be empty. Build a reference set and return annotated/novel counts plus novel IDs in observation order. Repeated observations are counted repeatedly.

novel=observed entries absent from annotation Set; annotatedCount=observedCount−novelCount

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

Output field	Meaning	Value type
annotatedCount	Annotated count	number
novelCount	Novel count	number
novelJunctionIds	Novel junction ids	list of string

json

{
  "input": {
    "observedJunctionIds": [
      "a",
      "b",
      "c"
    ],
    "annotatedJunctionIds": [
      "a",
      "c"
    ]
  },
  "output": {
    "annotatedCount": 2,
    "novelCount": 1,
    "novelJunctionIds": [
      "b"
    ]
  }
}

Limitations and assumptions

No genomic annotation lookup, coordinate normalization or read-support threshold is applied. Annotation duplicates do not change membership, but observed duplicates affect totals.

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 Canonical Splice Support: Count canonical GT–AG splice junction motifs. For a complementary task, use Backsplice Support: Tally back-splice junction reads supporting a circular RNA.

References

Junction Annotation Tally — tool.io

Similar or alternative tools

Canonical Splice Support
Count canonical GT–AG splice junction motifs.
Backsplice Support
Tally back-splice junction reads supporting a circular RNA.