Nucleosome-Free Fraction
Calculate the ATAC nucleosome-free fragment fraction.
Description
A nucleosome-free fraction summarizes a read class already assigned upstream.
A nucleosome-free fraction summarizes a read class already assigned upstream.1
Calculate the ATAC nucleosome-free fragment fraction.
When to use Nucleosome-Free Fraction
Use this tool to calculate the ATAC nucleosome-free fragment fraction.
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-Free Fraction 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 nucleosomeFreeFragments, totalFragments using the field table and calculation rules, then run the tool.
- Read nucleosomeFreeFraction, nucleosomeFreePercent. 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 |
|---|---|---|---|
| nucleosomeFreeFragments | Nucleosome-free fragments | integer; minimum: 0 | Required |
| totalFragments | Total fragments | integer; minimum: 1 | Required |
Enter positive integer total and free integer count within total; return fraction and percentage.
fraction=free/total; percent=100fraction Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| nucleosomeFreeFraction | Nucleosome-free fraction | number; minimum: 0; maximum: 1 |
| nucleosomeFreePercent | Nucleosome-free percentage | number; minimum: 0; maximum: 100 |
{
"input": {
"nucleosomeFreeFragments": 600,
"totalFragments": 1000
},
"output": {
"nucleosomeFreeFraction": 0.6,
"nucleosomeFreePercent": 60
}
}Limitations and assumptions
No size classification or region detection is performed.
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 Band Classifier: Classify an insert size into nucleosome periodicity bands. For a complementary task, use ATAC FRiP Gate: Gate ATAC quality by fraction of reads in peaks.
References
-
Nucleosome-Free Fraction — tool.io
Similar or alternative tools
- Nucleosome Band Classifier
Classify an insert size into nucleosome periodicity bands.
- ATAC FRiP Gate
Gate ATAC quality by fraction of reads in peaks.