Super-Enhancer Stitching

Stitch enhancer intervals separated by a supplied maximum distance.

Description

Enhancer stitching groups nearby intervals; it does not by itself identify ranked super-enhancers.

Enhancer stitching groups nearby intervals; it does not by itself identify ranked super-enhancers.^[1]

Stitch enhancer intervals separated by a supplied maximum distance.

When to use Super-Enhancer Stitching

Use this tool to stitch enhancer intervals separated by a supplied maximum distance.

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 Super-Enhancer Stitching 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 enhancerStartsBp, enhancerEndsBp, maximumStitchDistanceBp using the field table and calculation rules, then run the tool.
Read stitchedRegionCount, stitchedLengthsBp, totalStitchedLengthBp. 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
enhancerStartsBp	Enhancer starts	list of number	Required
enhancerEndsBp	Enhancer ends	list of number	Required
maximumStitchDistanceBp	Maximum stitch distance	number; minimum: 0	Required

Enter nonempty aligned sorted starts/ends with start≤end and nonnegative gap. Merge overlaps and qualifying gaps using maximum end; return counts and end−start lengths.

merge when nextStart−currentEnd≤maximumGap

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

Output field	Meaning	Value type
stitchedRegionCount	Stitched region count	integer; minimum: 0
stitchedLengthsBp	Stitched region lengths (bp)	list of number
totalStitchedLengthBp	Total stitched length (bp)	number; minimum: 0

json

{
  "input": {
    "enhancerStartsBp": [
      0,
      150,
      500
    ],
    "enhancerEndsBp": [
      100,
      250,
      600
    ],
    "maximumStitchDistanceBp": 100
  },
  "output": {
    "stitchedRegionCount": 2,
    "stitchedLengthsBp": [
      250,
      100
    ],
    "totalStitchedLengthBp": 350
  }
}

Limitations and assumptions

No chromosome grouping, enrichment ranking or super-enhancer threshold is supplied. Lengths exclude a +1 adjustment.

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 DMR Window Merger: Merge adjacent DMR windows within a selected distance. For a complementary task, use ABC Linkage Rank: Rank enhancer-gene links by activity-by-contact score.

References

Super-Enhancer Stitching — tool.io

Similar or alternative tools

DMR Window Merger
Merge adjacent DMR windows within a selected distance.
ABC Linkage Rank
Rank enhancer-gene links by activity-by-contact score.