Evaluating the Performance of Peak Calling Algorithms Available for Intracellular G-Quadruplex Sequencing.

ABSTRACT: DNA G-quadruplexes (G4) are non-canonical DNA structures that play key roles in various biological processes. Antibody-dependent sequencing is an important tool for identifying intracellularly formed DNA G4s, and peak calling is a crucial step in processing the sequencing data. As the applicability of existing peak calling algorithms to intracellular G4 data has not been previously assessed, we systematically compared and evaluated these algorithms to determine those best suited for G4 detection. We selected seven representative candidates from 43 published peak calling algorithms for detailed evaluation. The performance of each candidate on six published intracellular G4 sequencing datasets (GSE107690, GSE145090, GSE133379, GSE178668ChIP-seq, GSE178668CUT&Tag, GSE221437) were assessed by

SUBMITTER: Wang Y 

PROVIDER: S-EPMC11818603 | biostudies-literature | 2025 Jan

REPOSITORIES: biostudies-literature