Fragment Shift Distance

Calculate bimodal strand-peak shift distance.

Description

Strand-peak separation is a simple fragment-shift estimate from identified peaks.

Strand-peak separation is a simple fragment-shift estimate from identified peaks.^[1]

Calculate bimodal strand-peak shift distance.

When to use Fragment Shift Distance

Use this tool to calculate bimodal strand-peak shift distance.

Prepare the already measured signals, counts, coordinates, fitted coefficients or sequence strings requested. Keep assay definitions, units, aligned lists and caller-selected thresholds consistent.

How to use Fragment Shift Distance and understand its results

Prepare the already measured signals, counts, coordinates, fitted coefficients or sequence strings requested. Keep assay definitions, units, aligned lists and caller-selected thresholds consistent.
Enter forwardStrandPeakBp, reverseStrandPeakBp using the field table and calculation rules, then run the tool.
Read fragmentShiftBp, estimatedFragmentLengthBp. 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
forwardStrandPeakBp	Forward-strand peak (bp)	number	Required
reverseStrandPeakBp	Reverse-strand peak (bp)	number	Required

Enter finite signed positions; return distance and the same estimate as fragment length.

distance=abs(forwardPeak−reversePeak)

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

Output field	Meaning	Value type
fragmentShiftBp	Bimodal shift distance (bp)	number; minimum: 0
estimatedFragmentLengthBp	Estimated fragment length (bp)	number; minimum: 0

json

{
  "input": {
    "forwardStrandPeakBp": 100,
    "reverseStrandPeakBp": 250
  },
  "output": {
    "fragmentShiftBp": 150,
    "estimatedFragmentLengthBp": 150
  }
}

Limitations and assumptions

No cross-correlation, peak detection or confidence interval is fitted.

Numeric inputs, where present, 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.

Alternative or Complementary methods

Use Phantom-Peak Quality: Rate fragment versus phantom cross-correlation peaks. For a complementary task, use NSC Quality: Calculate normalized strand cross-correlation and quality gate.

References

Fragment Shift Distance — tool.io

Similar or alternative tools

Phantom-Peak Quality
Rate fragment versus phantom cross-correlation peaks.
NSC Quality
Calculate normalized strand cross-correlation and quality gate.