Fig. 2: Accuracy of circlehunter.
From: Circlehunter: a tool to identify extrachromosomal circular DNA from ATAC-Seq data
A F1 score of multi segments ecDNA detection with varying mock ecDNA local depth at 100 bp read length and varying read length at 30× local depth. B F1 score of single-segment ecDNA detection with varying mock ecDNA local depth at 100 bp read length and varying read length at 30× local depth. Circlehunter-s: A true-positive result is considered when the circlehunter result covers 95% of the simulated ecDNA and has the same ligation structure; Circlehunter-b: A true-positive result is considered when the circlehunter result breakpoint confidential intervals cover simulated ecDNA breakpoint and have the same ligation structure; Circlefinder-s: A true-positive result is considered when the Circle_finder result covers 95% of the simulated ecDNA. C Distribution of 95% confidential interval length with varying read length at 30× local depth. D–F Identify results of GBM39, PC3, and COLO320DM cell lines. Blue is the validated result, and orange and green are the individual results of two biological replicates. The color of the numbers indicating the genomic position corresponds to the circles. The numbers outside the circles are the absolute positions of the validated ecDNA fragments on the genome. The numbers inside the circles are the errors of the ecDNA fragments identified by circlehunter relative to the validated positions.
