RRBS Fragment Range

Filter RRBS fragment lengths against selected size bounds.

Description

RRBS size screening applies a caller-selected fragment window.

RRBS size screening applies a caller-selected fragment window.^[1]

Filter RRBS fragment lengths against selected size bounds.

When to use RRBS Fragment Range

Use this tool to filter RRBS fragment lengths against selected size bounds.

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 RRBS Fragment Range 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 fragmentLengthsBp, minimumBp, maximumBp using the field table and calculation rules, then run the tool.
Read retainedIndexes, excludedIndexes, retainedPercent. 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
fragmentLengthsBp	Fragment lengths bp	list of number	Required
minimumBp	Minimum bp	number	Required
maximumBp	Maximum bp	number	Required

Enter nonempty nonnegative lengths and ordered finite bounds. Return passing zero-based indices and percentage.

pass=minimum≤length≤maximum

Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.

Output field	Meaning	Value type
retainedIndexes	Retained indexes	list of number
excludedIndexes	Excluded indexes	list of number
retainedPercent	Retained percent	number

json

{
  "input": {
    "fragmentLengthsBp": [
      40,
      100,
      300
    ],
    "minimumBp": 50,
    "maximumBp": 250
  },
  "output": {
    "retainedIndexes": [
      1
    ],
    "excludedIndexes": [
      0,
      2
    ],
    "retainedPercent": 33.33333333333333
  }
}

Limitations and assumptions

Bounds may be signed. No restriction digest, CpG enrichment or library quality is verified.

Numeric inputs, where present, must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Lists are limited to 100,000 entries; the rules above may require smaller limits. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.

Alternative or Complementary methods

Use WGBS Depth Filter: Filter WGBS cytosine sites by a caller-supplied coverage depth. For a complementary task, use Nucleosome Repeat Length: Estimate nucleosome repeat length from ordered periodicity peaks.

References

RRBS Fragment Range — tool.io

Similar or alternative tools

WGBS Depth Filter
Filter WGBS cytosine sites by a caller-supplied coverage depth.
Nucleosome Repeat Length
Estimate nucleosome repeat length from ordered periodicity peaks.