I have a very fundamental doubt in chip-seq analysis.
We get the chromosome, poistion and read count information from the bed files for Input and IP samples and based on the position I generate the peak plots.
Using HOMER, we use the script findPeaks and get the peak information as well. How do we compare this result with the plots generated from the read count information?
Is it the genomic positions of the chromosomes which we get through HOMER findpeak output needs to be compared with the peak plot generated based on read count or something else? Is this correct to decide the enriched peaks or something else?