Integrated profiling of circulating nucleosomes for monitoring transcriptional evolution and therapeutic resistance in breast cancer

This Zenodo repository contains BED files with H3K4me3 peak calls derived from cfChIP-seq data generated as part of the quality control analyses for the above study. These peak files provide the genomic locations of H3K4me3-marked regions and can be used to reproduce or further interrogate the cfChIP-seq quality assessment. Peak calling was performed using macs2 callpeak (version 2.1.1) using a false discovery rate of q = 0.05, -f BAMPE and narrow peak configurations. A matched ~10x WGS dataset of each cfChIP-seq sample was used as the input for normalisation purposes.