Hi guys,
I'm looking at ChIP-seq input DNA (sonicated chromatin) and I see big differences in mapped reads coverage between conditions (WT vs mutant of S.pombe ) at centromeres and sub-telomeric regions.
input DNA : test vs ctl (image generated with the CNV-seq package)
How can I interpret such differences ?
Is it copy number variation ? That would make sense at telomeres because there is a two-fold increase in coverage. But what about the centromeres ?
Could it be differences in chromatin accessibility impacting the sonication process ?
In general, how do you make a difference between chromatin accessibility changes or copy number variation ?
Any suggestion is welcome !
Thanks,
Carlo