I have started using ChIPQC, and noticed that the read counts reported by the ChIPQC report are consistently twice as large as counts reported by MACS2. I looked in the ChIPQC documentation and could not find a reason why. Likewise, I googled the issue and could not find a plausible explanation.
I am using the latest R and ChIPQC version (checked last Friday). My ChIP-seq files contain single-ended reads.
Thanks for your help.