Bisulfite Primer CpG Check
Count CpGs in bisulfite primer sequences against a supplied maximum.
Description
Literal primer CpGs provide one bisulfite-assay design check.
Literal primer CpGs provide one bisulfite-assay design check.1
Count CpGs in bisulfite primer sequences against a supplied maximum.
When to use Bisulfite Primer CpG Check
Use this tool to count CpGs in bisulfite primer sequences against a supplied maximum.
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 Bisulfite Primer CpG Check 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 forwardPrimer, reversePrimer, maximumCpgCount using the field table and calculation rules, then run the tool.
- Read forwardCpgCount, reverseCpgCount, totalCpgCount, passesConstraint. 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 |
|---|---|---|---|
| forwardPrimer | Forward primer | string | Required |
| reversePrimer | Reverse primer | string | Required |
| maximumCpgCount | Maximum CpG count | integer; minimum: 0 | Required |
Enter strings and nonnegative integer ceiling; return per-primer/total counts and inclusive total≤ceiling flag. Empty strings are accepted.
total=CG matches in uppercased forward and reverse strings Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| forwardCpgCount | Forward-primer CpGs | integer; minimum: 0 |
| reverseCpgCount | Reverse-primer CpGs | integer; minimum: 0 |
| totalCpgCount | Total primer CpGs | integer; minimum: 0 |
| passesConstraint | Within supplied CpG constraint | boolean |
{
"input": {
"forwardPrimer": "ATCGAT",
"reversePrimer": "TTTTAA",
"maximumCpgCount": 1
},
"output": {
"forwardCpgCount": 1,
"reverseCpgCount": 0,
"totalCpgCount": 1,
"passesConstraint": true
}
}Limitations and assumptions
No alphabet validation, reverse complement, melting temperature or alignment is performed.
Numeric inputs, where present, must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Extremely large text inputs are rejected. 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 MSP Product Size: Validate an MSP product size against an expected amplicon and tolerance. For a complementary task, use Methylation Context: Classify a cytosine as CG, CHG, or CHH context.
References
-
Bisulfite Primer CpG Check — tool.io
Similar or alternative tools
- MSP Product Size
Validate an MSP product size against an expected amplicon and tolerance.
- Methylation Context
Classify a cytosine as CG, CHG, or CHH context.