Dear All,

We are trying to analyse some ChIP seq data sets on one of the repeated regions of Genome (Ribosomal DNA). Recently one paper defined the pipeline for this region, upon following the pipeline we are not getting the tracks as expected for the data set already used in the paper. Upon following the whole pipeline we are getting same tracks for our input and IP.We suspect that we are getting wrong in the BamCoverage command. For further convenience, we have attached the link of the manuscript which we are following. Also we have attached the screen shot of tracks.

Link for the paper https://doi.org/10.1016/j.jbc.2023.104766