Han Chu

Nov 10, 2023 | bmcgenomics.biomedcentral.com | Hansen Cheng |Wenhao Ma |Kun Wang |Han Chu |Yu Ren Liao |Yawen Yuan | +5 more

The bulk ATAC-seq and WGS data of PC3, COLO320DM, and SNU16 cells and single cell ATAC-seq data of COLO320DM cells were collected with the source and ID numbers (Table S1). These cell lines have been validated for ecDNA regions (Table S2) [3, 9, 19]. The sequence files in the fastq format were pre-processed and indexed using fastp [20], BWA [21], and SAMtools [22]. The ATACAmp workflow is shown in Fig. 1B and comprises the following steps.