Hi all,

I am new to Diffbind and following the workflow from the handbook: https://bioconductor.org/packages/devel/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf I used HMMRATAC to generate the peak files, instead of MACS2. So I used the HMMRATAC output .summit (BED 5 : chr, start, end, peak_name, score) to generate the dba object. it's fine to plot the correlation heatmap on peak caller score.

But when I try to run dba.count() using my own dataset I get the following output messages and error

peakset_count<-dba.count(peakset)

Computing summits...

Re-centering peaks...

Reads will be counted as Paired-end.

Reads will be counted as Paired-end.

Reads will be counted as Paired-end.

Reads will be counted as Paired-end.

Reads will be counted as Paired-end.

Reads will be counted as Paired-end.

Error in DESeqDataSet(se, design = design, ignoreRank) :all samples have 0 counts for all genes. check the counting script.

what is it that went wrong ? my Diffbind version is (DiffBind_3.4.11) Thanks