Hi! I am new in galaxy and I am trying to analyse the sequences of a ChIP-Seq.I have been reading a lot of tutorials for that but I am getting stuck. I have two ChIP-Seq samples, with a Mnase fragmentation, one is the biological control sample (not the input) and the other one is the treated sample. We didn't sequence the input so I can't use it for eliminate the background in the data analysis. So how can I do the peak calling step? I don't think that using the biological control I will get a good result of peaks, and I don't know what is the correct way of doing it. Any help is more than welcome! Thanks
Both are routinely used in experiments, including those done by the ENCODE consortium. Example article describing the processing (there are many others): http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431496/
Peaks can also be called with just the single treatment sample. Perhaps run an experiment to see how the results differ: run once with just the treatment, once with the treatment + control, and then compare the two? In the end, this will be a judgement call on your part, but running a few tests will provide more information to base the final protocol decisions on.
Best, Jen, Galaxy team