Phantom-Peak Quality
Rate fragment versus phantom cross-correlation peaks.
Description
Fragment and phantom cross-correlation peaks support sequencing-quality review.
Fragment and phantom cross-correlation peaks support sequencing-quality review.1
Rate fragment versus phantom cross-correlation peaks.
When to use Phantom-Peak Quality
Use this tool to rate fragment versus phantom cross-correlation peaks.
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 Phantom-Peak Quality 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 fragmentPeakCorrelation, phantomPeakCorrelation, minimumRsc using the field table and calculation rules, then run the tool.
- Read relativeStrandCorrelation, phantomPeakRatio, passesGate. 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 |
|---|---|---|---|
| fragmentPeakCorrelation | Fragment peak correlation | number; minimum: 0 | Required |
| phantomPeakCorrelation | Phantom peak correlation | number; minimum: 0 | Required |
| minimumRsc | Minimum relative strand correlation | number; minimum: 0 | Required |
Enter positive peaks and nonnegative minimum ratio. Return both ratios and inclusive gate.
ratio=fragmentPeak/phantomPeak; reciprocal=phantomPeak/fragmentPeak Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| relativeStrandCorrelation | Relative strand correlation | number; minimum: 0 |
| phantomPeakRatio | Phantom-to-fragment peak ratio | number; minimum: 0 |
| passesGate | Passes phantom-peak gate | boolean |
{
"input": {
"fragmentPeakCorrelation": 0.2,
"phantomPeakCorrelation": 0.1,
"minimumRsc": 1.5
},
"output": {
"relativeStrandCorrelation": 2,
"phantomPeakRatio": 0.5,
"passesGate": true
}
}Limitations and assumptions
This simple ratio is not the background-adjusted relative strand correlation formula. No curve is computed.
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. A successfully returned false flag is an evaluated outcome; its meaning is explained above.
Alternative or Complementary methods
Use NSC Quality: Calculate normalized strand cross-correlation and quality gate. For a complementary task, use Fragment Shift Distance: Calculate bimodal strand-peak shift distance.
References
-
Phantom-Peak Quality — tool.io
Similar or alternative tools
- NSC Quality
Calculate normalized strand cross-correlation and quality gate.
- Fragment Shift Distance
Calculate bimodal strand-peak shift distance.