Nucleosome Band Classifier
Classify an insert size into nucleosome periodicity bands.
Description
Periodic ATAC fragment bands can be compared with fixed reference centers.
Periodic ATAC fragment bands can be compared with fixed reference centers.1
Classify an insert size into nucleosome periodicity bands.
When to use Nucleosome Band Classifier
Use this tool to classify an insert size into nucleosome periodicity bands.
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 Nucleosome Band Classifier 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 insertSizeBp, bandToleranceBp using the field table and calculation rules, then run the tool.
- Read bandClass, nearestBandDistanceBp. 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 |
|---|---|---|---|
| insertSizeBp | Insert size (bp) | number; minimum: 0 | Required |
| bandToleranceBp | Band tolerance (bp) | number; minimum: 0 | Required |
Enter nonnegative length/tolerance. Return nearest distance and band when within tolerance, otherwise other. Ties favor the earlier center.
nearest of [0,200,400]; match when distance≤tolerance Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| bandClass | Nucleosome band | string; one of "nucleosome-free", "mono-nucleosome", "di-nucleosome", "other" |
| nearestBandDistanceBp | Distance to nearest band (bp) | number; minimum: 0 |
{
"input": {
"insertSizeBp": 210,
"bandToleranceBp": 25
},
"output": {
"bandClass": "mono-nucleosome",
"nearestBandDistanceBp": 10
}
}Limitations and assumptions
No distribution fit or occupancy is inferred.
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.
Alternative or Complementary methods
Use Nucleosome-Free Fraction: Calculate the ATAC nucleosome-free fragment fraction. For a complementary task, use Nucleosome Repeat Length: Estimate nucleosome repeat length from ordered periodicity peaks.
References
-
Nucleosome Band Classifier — tool.io
Similar or alternative tools
- Nucleosome-Free Fraction
Calculate the ATAC nucleosome-free fragment fraction.
- Nucleosome Repeat Length
Estimate nucleosome repeat length from ordered periodicity peaks.