Hi again! I was wondering, when I call peaks with MACS using my treatment and control, I get 1600 peaks. However, when I call the peaks using treatment or control only, I get treatment (350 peaks) and control (600 peaks). I was under the impression that it should have given me a larger number of peaks for my treatment only sample, and that the treatment + control peaks are basically the peaks from the ;control sample only' subtracted from the 'treatment only' sample. Could you please explain me why is this so? Please forgive my ignorance, I am very new at this stuff. Thanks!
The control is reducing the number of "false peaks" (exist as a background) when used with the treated sample. Use a control whenever possible. You can play around with the parameters and compare the different results, along with a reference annotation - if you have one - to better interpret the differences. Try visualizing all results in a browser for a distinct genome region or two (zoom into a region) to make this comparison less complex.
The baseline peaks are called using mapped BAM(s) plus the parameters set for the tool. Calling peaks with just the input or treated sample alone can produce in spurious peak calling. Also, parameters work best when used in combinations that target a specific peak calling goal. Try the recommended combinations from the tool form help (including the tool manual) and compare the results to those obtained when using your own settings.
This is related to your other question and I encourage you to review the tool documentation and explore the MACS2 wiki and google group to better understand how it works. The full suite of MACS2 tools/functions are incorporated into Galaxy and line command usage can be replicated with the Galaxy wrappers around these tools/tool form options. https://biostar.usegalaxy.org/p/26967/
All of this assumes that mapping went well and that there are no technical errors (incorrect or different genome mapped against for one of the mapping runs, and other common usage issues). https://galaxyproject.org/support/#troubleshooting
Thanks! Jen, Galaxy team