Backsplice Support

Tally back-splice junction reads supporting a circular RNA.

Description

A back-splice coordinate screen counts donor positions numerically above acceptor positions.

A back-splice coordinate screen counts donor positions numerically above acceptor positions. Its interpretation depends on strand and coordinate conventions established upstream.^[1]

Tally back-splice junction reads supporting a circular RNA.

When to use Backsplice Support

Use this tool to tally back-splice junction reads supporting a circular RNA.

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 Backsplice Support 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 donorCoordinates, acceptorCoordinates, minimumSupport using the field table and calculation rules, then run the tool.
Read backspliceIndexes, supportCount, supported. 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
donorCoordinates	Donor coordinates	list of number	Required
acceptorCoordinates	Acceptor coordinates	list of number	Required
minimumSupport	Minimum support	number	Required

Enter aligned nonempty finite donor/acceptor lists and minimum support at least one. Return zero-based indices satisfying the strict ordering, support count and inclusive threshold flag. Equal coordinates are not counted.

backsplice if donorCoordinate>acceptorCoordinate; supported if count≥minimumSupport

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

Output field	Meaning	Value type
backspliceIndexes	Backsplice indexes	list of number
supportCount	Support count	number
supported	Supported	boolean

json

{
  "input": {
    "donorCoordinates": [
      200,
      100,
      200
    ],
    "acceptorCoordinates": [
      100,
      200,
      100
    ],
    "minimumSupport": 2
  },
  "output": {
    "backspliceIndexes": [
      0,
      2
    ],
    "supportCount": 2,
    "supported": true
  }
}

Limitations and assumptions

The comparison does not inspect alignments, strand, chromosome or mapping quality and therefore does not prove circular RNA. Coordinate and support values need not be integers in the schema.

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. A successfully returned false flag is an evaluated outcome; its meaning is explained above.

Alternative or Complementary methods

Use Junction Annotation Tally: Tally annotated versus novel observed splice junctions. For a complementary task, use Fusion Breakpoint Support: Count read pairs spanning a caller-specified fusion breakpoint.

References

Backsplice Support — tool.io

Similar or alternative tools

Junction Annotation Tally
Tally annotated versus novel observed splice junctions.
Fusion Breakpoint Support
Count read pairs spanning a caller-specified fusion breakpoint.