Data and code for ecDNA detected from patients

Repository Structure: Code_ecDNA-main.zip This repository contains four main directories containing the scripts, raw data, and analytical outputs required for eccDNA processing, quality control, graph generation, and genomic annotation. 1. Circlemap Contains scripts and data files related to eccDNA processing. Circlemap.sh: Bash script for processing eccDNA using the Circlemap tool. *_circle.bed: Raw BED files generated by Circlemap for each individual sequencing dataset. *_circle_filter.bed: Refined BED files, filtered according to the study's specific selection criteria. 2. FastQC Contains scripts and outputs for the quality control (QC) of the sequencing data. QC.sh: Bash script for executing quality control processing on the sequencing datasets. stat_samtools.txt: Summary statistics for each sequencing dataset post-alignment to the human reference genome. *_fastqc.html: Visual HTML reports generated by FastQC. 3. Graph_code Contains the R codebase used for visual data representation. R scripts: Code utilized for conducting ChIPseeker analysis and generating visualizations using each sequencing dataset as input. The resulting graphs correspond to Figure 3F in the manuscript. 4. HOMER Contains scripts and data related to genomic feature and repeat annotations. Repeat.sh: Bash script for annotating eccDNA repeats utilizing bedtools. HOMER.sh: Bash script for annotating eccDNA genomic features utilizing HOMER's annotatePeaks.pl. *_combined_filter.bed: Aggregated BED files, compiled from all filtered datasets and classified by tumor type. *_filter_overlap_count.bed: Output BED files generated by the Repeat.sh script. *_homer.txt: Detailed HOMER annotation files generated by the HOMER.sh script. *_homer_states.txt: Summary statistics of the HOMER annotations generated by the HOMER.sh script.