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annaos 06-04-2018 02:04 PM

ChIP-seq peaks in centromeric regions

I am struggling with non specific peaks called by macs2 around centromeric regions in my ChIP-seq data. A lot of reads map around these regions on all chromosomes, and here hundreds of peaks are called, even if the signal of the input control is weirdly the same. This is the first time I see this happening and I have a fair experience with ChIP-seq data.
After the alignment and QC, I have quality-trimmed reads, removed duplicates, and filtered for blacklisted regions. Tried to play with q-value and other flags in macs2 but can't get rid of these fake peaks. Any idea?

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