Bisulfite Conversion Efficiency
Check bisulfite conversion efficiency from non-CpG cytosines.
Description
Conversion efficiency summarizes converted observations relative to an assessed total.
Conversion efficiency summarizes converted observations relative to an assessed total.1
Check bisulfite conversion efficiency from non-CpG cytosines.
When to use Bisulfite Conversion Efficiency
Use this tool to check bisulfite conversion efficiency from non-CpG cytosines.
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 Conversion Efficiency 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 convertedNonCpgCs, totalNonCpgCs, minimumConversionPercent using the field table and calculation rules, then run the tool.
- Read conversionPercent, unconvertedCount, passes. 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 |
|---|---|---|---|
| convertedNonCpgCs | Converted non cpg cs | number | Required |
| totalNonCpgCs | Total non cpg cs | number | Required |
| minimumConversionPercent | Minimum conversion percent | number | Required |
Enter positive total, converted within total and finite minimum percent. Return efficiency/unconverted amount and inclusive gate.
efficiency%=100converted/total Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| conversionPercent | Conversion percent | number |
| unconvertedCount | Unconverted count | number |
| passes | Passes | boolean |
{
"input": {
"convertedNonCpgCs": 90,
"totalNonCpgCs": 100,
"minimumConversionPercent": 95
},
"output": {
"conversionPercent": 90,
"unconvertedCount": 10,
"passes": false
}
}Limitations and assumptions
Fractional counts and thresholds outside 0–100 are accepted. No experiment or sequencing bias is assessed.
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 Single-CpG Methylation: Calculate single-CpG methylation after background correction. For a complementary task, use COBRA Retention: Calculate COBRA restriction cut-site retention from band intensities.
References
-
Bisulfite Conversion Efficiency — tool.io
Similar or alternative tools
- Single-CpG Methylation
Calculate single-CpG methylation after background correction.
- COBRA Retention
Calculate COBRA restriction cut-site retention from band intensities.