I have no expertise in bioinformatics and I’m analyzing ChIP seq data from histone markers. Since I have no input of my sample, after mapping I normalized it with BamCoverage (calculating my own scale factor with spike-in reads) and I called peaks with MACS. My output is in bedgraph format after normalization and after peak calling and now I am not able to annotate the peaks with gene names with ChIPseeker or other servers as GREAT. It just a format issue? I also tried an annotation with bed files from MACS without previous normalization but still not working.
What am I doing wrong?
Thanks a million