FRiP

FRiP, or fraction of reads in peaks, is a commonly used quality metric in chromatin immunoprecipitation followed by sequencing (ChIP-seq) experiments. It quantifies the proportion of reads that fall within regions identified as peaks relative to the total number of reads mapped to the genome. The numerator counts reads overlapping the union of called peaks, while the denominator uses the total mapped reads, often after duplicate removal. Peak calling is typically performed with software such as MACS2, using a specified statistical threshold, and FRiP can be computed using peak calls generated for a given sample or a common peak set for cross-sample comparisons.

Interpretation and usage: A higher FRiP indicates greater enrichment and a stronger signal-to-noise ratio, and it is frequently used as a quick QC check and to compare samples within the same experiment. However, FRiP is influenced by sequencing depth, peak-calling parameters, and genome mappability, and it is not directly comparable across experiments with differing depths or peak definitions. It is best used alongside other quality metrics such as normalized strand cross-correlation (NSC) and relative cross-correlation (RSC), transcription start site (TSS) enrichment, and library complexity.

Limitations: For broad histone marks, FRiP values can be lower even in high-quality data because peak regions are diffuse. Comparisons across laboratories or studies should use consistent processing and consider depth normalization. See also related ChiP-seq quality metrics and peak-calling guidelines.