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Hey, I have recently acquired what looks like good RNA Polymerase II Chip-Seq data. I was looking for tools for normalization etc. Usually I use Homer or Macs2 for peak-calling, but they don't seem to be ideal for Pol2 ChIP-Seq analysis. I was wondering if anyone used the Polyphemus R package?(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3287170/).
If not, you can also provide info on the tools you use for RNA Polymerase II ChIP-Seq.
If not, you can also provide info on the tools you use for RNA Polymerase II ChIP-Seq.