MSP Product Size
Validate an MSP product size against an expected amplicon and tolerance.
Description
Amplicon-size agreement is one check on a methylation-specific PCR product.
Amplicon-size agreement is one check on a methylation-specific PCR product.1
Validate an MSP product size against an expected amplicon and tolerance.
When to use MSP Product Size
Use this tool to validate an MSP product size against an expected amplicon and tolerance.
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 MSP Product Size 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 expectedProductBp, observedProductBp, sizeToleranceBp using the field table and calculation rules, then run the tool.
- Read sizeDifferenceBp, absoluteDifferenceBp, validProductSize. 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 |
|---|---|---|---|
| expectedProductBp | Expected MSP product size (bp) | integer; minimum: 0 | Required |
| observedProductBp | Observed MSP product size (bp) | integer; minimum: 0 | Required |
| sizeToleranceBp | Allowed size tolerance (bp) | integer; minimum: 0 | Required |
Enter nonnegative integer lengths/tolerance; return signed difference and inclusive gate.
difference=observed−expected; pass=abs(difference)≤tolerance Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| sizeDifferenceBp | Observed minus expected size (bp) | integer |
| absoluteDifferenceBp | Absolute size difference (bp) | integer; minimum: 0 |
| validProductSize | Within supplied size tolerance | boolean |
{
"input": {
"expectedProductBp": 150,
"observedProductBp": 153,
"sizeToleranceBp": 5
},
"output": {
"sizeDifferenceBp": 3,
"absoluteDifferenceBp": 3,
"validProductSize": true
}
}Limitations and assumptions
No primer alignment, sequence identity or methylation call is established.
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 Bisulfite Primer CpG Check: Count CpGs in bisulfite primer sequences against a supplied maximum. For a complementary task, use Methylation Context: Classify a cytosine as CG, CHG, or CHH context.
References
-
MSP Product Size — tool.io
Similar or alternative tools
- Bisulfite Primer CpG Check
Count CpGs in bisulfite primer sequences against a supplied maximum.
- Methylation Context
Classify a cytosine as CG, CHG, or CHH context.