FRiP Score
Calculate fraction of mapped reads in peaks.
Description
FRiP is the share of reads assigned to an existing peak set.
FRiP is the share of reads assigned to an existing peak set.1
Calculate fraction of mapped reads in peaks.
When to use FRiP Score
Use this tool to calculate fraction of mapped 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 FRiP Score 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, totalMappedReads using the field table and calculation rules, then run the tool.
- Read fripFraction, fripPercent. 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 |
| totalMappedReads | Total mapped reads | integer; minimum: 1 | Required |
Enter positive integer total and integer peak reads within total; return fraction/percentage.
fraction=peakReads/total; percent=100fraction Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| fripFraction | FRiP fraction | number; minimum: 0; maximum: 1 |
| fripPercent | FRiP percentage | number; minimum: 0; maximum: 100 |
{
"input": {
"readsInPeaks": 250,
"totalMappedReads": 1000
},
"output": {
"fripFraction": 0.25,
"fripPercent": 25
}
}Limitations and assumptions
No peaks or overlaps are computed and no quality threshold 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.
Alternative or Complementary methods
Use ATAC FRiP Gate: Gate ATAC quality by fraction of reads in peaks. For a complementary task, use TSS Enrichment Gate: Calculate TSS enrichment and gate against a supplied minimum.
References
-
FRiP Score — tool.io
Similar or alternative tools
- ATAC FRiP Gate
Gate ATAC quality by fraction of reads in peaks.
- TSS Enrichment Gate
Calculate TSS enrichment and gate against a supplied minimum.