DNase Footprint Depth
Measure DNase footprint depth relative to flanks.
Description
A DNase footprint can show reduced central signal relative to its flanks.
A DNase footprint can show reduced central signal relative to its flanks.1
Measure DNase footprint depth relative to flanks.
When to use DNase Footprint Depth
Use this tool to measure DNase footprint depth relative to flanks.
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 DNase Footprint Depth 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 leftFlank, centerSignal, rightFlank, minimumDepthPercent using the field table and calculation rules, then run the tool.
- Read depthPercent, protected. 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 |
|---|---|---|---|
| leftFlank | Left flank signal | number; minimum: 0 | Required |
| centerSignal | Footprint signal | number; minimum: 0 | Required |
| rightFlank | Right flank signal | number; minimum: 0 | Required |
| minimumDepthPercent | Minimum depth | number; minimum: 0 | Required |
Enter nonnegative signals with positive flank mean and nonnegative minimum depth. Return depth and inclusive flag.
depth%=100(1−center/mean(flanks)) Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| depthPercent | Footprint depth (%) | number |
| protected | Protected footprint | boolean |
{
"input": {
"leftFlank": 100,
"centerSignal": 40,
"rightFlank": 100,
"minimumDepthPercent": 50
},
"output": {
"depthPercent": 60,
"protected": true
}
}Limitations and assumptions
Depth may be negative. No motif, cleavage-bias correction or significance is assessed.
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. A successfully returned false flag is an evaluated outcome; its meaning is explained above.
Alternative or Complementary methods
Use Peak Summit: Record a ChIP-seq peak summit from positional read counts. For a complementary task, use CRISPR Off-Target Count: Count CRISPR epigenome-editing off-targets by mismatch risk threshold.
References
-
DNase Footprint Depth — tool.io
Similar or alternative tools
- Peak Summit
Record a ChIP-seq peak summit from positional read counts.
- CRISPR Off-Target Count
Count CRISPR epigenome-editing off-targets by mismatch risk threshold.