TSS Enrichment Gate
Calculate TSS enrichment and gate against a supplied minimum.
Description
TSS enrichment compares a central signal with background under a selected assay criterion.
TSS enrichment compares a central signal with background under a selected assay criterion.1
Calculate TSS enrichment and gate against a supplied minimum.
When to use TSS Enrichment Gate
Use this tool to calculate TSS enrichment and gate against a supplied minimum.
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 TSS Enrichment Gate 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 tssCenterSignal, flankingBackgroundSignal, minimumEnrichment using the field table and calculation rules, then run the tool.
- Read tssEnrichment, enrichmentMargin, passesGate. 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 |
|---|---|---|---|
| tssCenterSignal | TSS center signal | number; minimum: 0 | Required |
| flankingBackgroundSignal | Flanking background | number; minimum: 0 | Required |
| minimumEnrichment | Minimum enrichment | number; minimum: 0 | Required |
Enter nonnegative center/minimum and positive background. Return ratio, signed margin and inclusive gate.
ratio=center/background; margin=ratio−minimum Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| tssEnrichment | TSS enrichment | number; minimum: 0 |
| enrichmentMargin | Enrichment margin | number |
| passesGate | Passes gate | boolean |
{
"input": {
"tssCenterSignal": 100,
"flankingBackgroundSignal": 10,
"minimumEnrichment": 8
},
"output": {
"tssEnrichment": 10,
"enrichmentMargin": 2,
"passesGate": true
}
}Limitations and assumptions
No profile, intervals or assay-specific quality standard is inferred.
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 ATAC FRiP Gate: Gate ATAC quality by fraction of reads in peaks. For a complementary task, use FRiP Score: Calculate fraction of mapped reads in peaks.
References
-
TSS Enrichment Gate — tool.io
Similar or alternative tools
- ATAC FRiP Gate
Gate ATAC quality by fraction of reads in peaks.
- FRiP Score
Calculate fraction of mapped reads in peaks.