I am a beginner in chip-seq analysis.
I am trying to find a set of peaks for cancer data. The data that I have include 2 samples (health and cancerous sample). I would like to use MACS for peak calling.
my question is:
For peak calling if there is a healthy and cancerous chip seq data, can we use healthy sample as CONTROL ?
OR it is wrong? because the healthy sample is not the INPUT data I am confused.
any tip is highly appreciated.