I have now been through my ChIP-Seq analyses with some success using the Galaxy platform up to visualization of peak in UCSC. I identify a couple of interesting region that will validate by ChIP-qPCR based on the qualitative difference between treated and non-treated or IP non-treated and INPUT non-treated. I was wondering if there is a way to perform quantification in a more formaly (with statistics?). First, I was thinking about how many reads actually support my claim. How can I visually map the exact read behind the peaks?
Any help is always appreciate as usual,