Fusion Breakpoint Support

Count read pairs spanning a caller-specified fusion breakpoint.

Description

Breakpoint support can screen paired coordinates near supplied left/right targets.

Breakpoint support can screen paired coordinates near supplied left/right targets. The coordinate test is a proxy distinct from identifying a fusion in alignment data.^[1]

Count read pairs spanning a caller-specified fusion breakpoint.

When to use Fusion Breakpoint Support

Use this tool to count read pairs spanning a caller-specified fusion breakpoint.

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 Fusion Breakpoint 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 readLeftCoordinates, readRightCoordinates, leftBreakpoint, rightBreakpoint, breakpointTolerance using the field table and calculation rules, then run the tool.
Read supportingReadIndexes, supportCount. 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
readLeftCoordinates	Read left coordinates	list of number	Required
readRightCoordinates	Read right coordinates	list of number	Required
leftBreakpoint	Left breakpoint	number	Required
rightBreakpoint	Right breakpoint	number	Required
breakpointTolerance	Breakpoint tolerance	number	Required

Enter aligned nonempty coordinate lists, both breakpoints and nonnegative tolerance using a shared coordinate convention. Return zero-based indices meeting all three comparisons and their count. Equal left/right coordinates do not support.

support if |left−leftBreakpoint|≤tolerance AND |right−rightBreakpoint|≤tolerance AND left<right

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

Output field	Meaning	Value type
supportingReadIndexes	Supporting read indexes	list of number
supportCount	Support count	number

json

{
  "input": {
    "readLeftCoordinates": [
      90,
      50,
      99
    ],
    "readRightCoordinates": [
      110,
      95,
      101
    ],
    "leftBreakpoint": 100,
    "rightBreakpoint": 100,
    "breakpointTolerance": 10
  },
  "output": {
    "supportingReadIndexes": [
      0,
      2
    ],
    "supportCount": 2
  }
}

Limitations and assumptions

This assumes comparable numeric axes and does not model chromosome labels, strand, split alignments or mapping quality. It does not establish a biological fusion or its significance.

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 Backsplice Support: Tally back-splice junction reads supporting a circular RNA. For a complementary task, use Junction Annotation Tally: Tally annotated versus novel observed splice junctions.

References

Fusion Breakpoint Support — tool.io

Similar or alternative tools

Backsplice Support
Tally back-splice junction reads supporting a circular RNA.
Junction Annotation Tally
Tally annotated versus novel observed splice junctions.