Hydroxymethylation Subtraction
Subtract oxBS from BS methylation to estimate 5hmC.
Description
Paired BS/oxBS measurements can separate a hydroxymethylation component under compatible assay assumptions.
Paired BS/oxBS measurements can separate a hydroxymethylation component under compatible assay assumptions.1
Subtract oxBS from BS methylation to estimate 5hmC.
When to use Hydroxymethylation Subtraction
Use this tool to subtract oxBS from BS methylation to estimate 5hmC.
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 Hydroxymethylation Subtraction 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 bsMethylationPercent, oxbsMethylationPercent using the field table and calculation rules, then run the tool.
- Read hydroxymethylationPercent, methylcytosinePercent, consistent. 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 |
|---|---|---|---|
| bsMethylationPercent | Bs methylation percent | number | Required |
| oxbsMethylationPercent | Oxbs methylation percent | number | Required |
Enter percentages 0–100; return components and consistent flag BS≥oxBS.
5hmC=max(0,BS−oxBS); 5mC=oxBS Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| hydroxymethylationPercent | Hydroxymethylation percent | number |
| methylcytosinePercent | Methylcytosine percent | number |
| consistent | Consistent | boolean |
{
"input": {
"bsMethylationPercent": 70,
"oxbsMethylationPercent": 40
},
"output": {
"hydroxymethylationPercent": 30,
"methylcytosinePercent": 40,
"consistent": true
}
}Limitations and assumptions
No conversion efficiency, assay bias or uncertainty is corrected.
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 TET Cascade Stage: Map a cytosine modification to its TET cascade stage. For a complementary task, use Single-CpG Methylation: Calculate single-CpG methylation after background correction.
References
-
Hydroxymethylation Subtraction — tool.io
Similar or alternative tools
- TET Cascade Stage
Map a cytosine modification to its TET cascade stage.
- Single-CpG Methylation
Calculate single-CpG methylation after background correction.