Hello forum

I am trying to conduct a H3K27ac ChIP-seq analysis in Diffbind version 3.16 in R, but every time i try using dba.count to generate the count matrix, I "lose" peak regions due to default mergeing of overlapping peak regions by dba.count (the same peak region is specified and set for each sample and replicate). I have provided my code below. Does anyone have an idea for a solution or work-around for the problem? Help is much appreciated

#Load sample sheet made in excel
sample_sheet <- read.csv2(file.path("Sample sheet H3K27ac TBX3 OE vs CTRL.csv"))

sample_sheet

#Load DiffBind
library(DiffBind)

#Create DBA object using "dba()" specifying sample sheet
TBX3_OE_H3K27ac_dba <- dba(sampleSheet = sample_sheet)

TBX3_OE_H3K27ac_dba

#Run dba.count without using summit centering
TBX3_OE_H3K27ac_dba_count <- dba.count(
  TBX3_OE_H3K27ac_dba,
  summits = FALSE, bUseSummarizeOverlaps = TRUE
)

TBX3_OE_H3K27ac_dba_count