Hello biostars,

I am new to this type of analysis. I have IDR.NarrowPeak data and I would like to normalise it to FPKM using R.
I read that the packages limma and DESeq are helpful but I still have problems creating the count matrix.
Is there a step I am missing?
 
Any help/suggestion will be appreciated.
You should try DiffBind, which uses DESeq and edgeR in the background and automates this process: https://bioconductor.org/packages/release/bioc/html/DiffBind.html
