ATAC FRiP Gate
Gate ATAC quality by fraction of reads in peaks.
Description
ATAC FRiP gating screens a supplied peak-read share under a chosen percentage.
ATAC FRiP gating screens a supplied peak-read share under a chosen percentage.1
Gate ATAC quality by fraction of reads in peaks.
When to use ATAC FRiP Gate
Use this tool to gate ATAC quality by fraction of reads in peaks.
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 ATAC FRiP 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 readsInPeaks, mappedReads, minimumFripPercent using the field table and calculation rules, then run the tool.
- Read fripPercent, 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 |
|---|---|---|---|
| readsInPeaks | Reads in peaks | integer; minimum: 0 | Required |
| mappedReads | Mapped reads | integer; minimum: 1 | Required |
| minimumFripPercent | Minimum FRiP | number; minimum: 0; maximum: 100 | Required |
Enter positive integer total, integer peak reads within total and nonnegative minimum; return percent/gate.
FRiP%=100peakReads/total; pass=FRiP%≥minimum Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| fripPercent | FRiP | number; minimum: 0; maximum: 100 |
| passesGate | Passes FRiP gate | boolean |
{
"input": {
"readsInPeaks": 300,
"mappedReads": 1000,
"minimumFripPercent": 20
},
"output": {
"fripPercent": 30,
"passesGate": true
}
}Limitations and assumptions
No peak calling, overlaps or universal assay-quality verdict is supplied.
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 FRiP Score: Calculate fraction of mapped reads in peaks. For a complementary task, use TSS Enrichment Gate: Calculate TSS enrichment and gate against a supplied minimum.
References
-
ATAC FRiP Gate — tool.io
Similar or alternative tools
- FRiP Score
Calculate fraction of mapped reads in peaks.
- TSS Enrichment Gate
Calculate TSS enrichment and gate against a supplied minimum.