Peak Summit
Record a ChIP-seq peak summit from positional read counts.
Description
A supplied peak summit is the strongest sampled observation in a region.
A supplied peak summit is the strongest sampled observation in a region.1
Record a ChIP-seq peak summit from positional read counts.
When to use Peak Summit
Use this tool to record a ChIP-seq peak summit from positional read counts.
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 Peak Summit 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 positionsBp, readCounts using the field table and calculation rules, then run the tool.
- Read summitPositionBp, summitReadCount, readsPerPosition. 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 |
|---|---|---|---|
| positionsBp | Peak positions (bp) | list of number | Required |
| readCounts | Read counts | list of number | Required |
Enter nonempty aligned finite positions and nonnegative counts. Return first maximum position and mean count.
summit=position of first maximum count Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| summitPositionBp | Peak summit position (bp) | number |
| summitReadCount | Summit read count | number; minimum: 0 |
| readsPerPosition | Mean reads per position | number; minimum: 0 |
{
"input": {
"positionsBp": [
100,
110,
120
],
"readCounts": [
5,
20,
10
]
},
"output": {
"summitPositionBp": 110,
"summitReadCount": 20,
"readsPerPosition": 11.666666666666666
}
}Limitations and assumptions
Positions may be unsorted and counts fractional. No peak calling or interpolation is performed.
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 Fragment Shift Distance: Calculate bimodal strand-peak shift distance. For a complementary task, use DNase Footprint Depth: Measure DNase footprint depth relative to flanks.
References
-
Peak Summit — tool.io
Similar or alternative tools
- Fragment Shift Distance
Calculate bimodal strand-peak shift distance.
- DNase Footprint Depth
Measure DNase footprint depth relative to flanks.