Hello Everyone, I have a tiny question about macs2, I'm not sure I've understand the different output it produces... For example what are peaks.narrowpeaks files and why are we chossing this one for bedtools intersect ? I'm sorry but I just didn't get the point ?? And is there anything to improve macs2 analysis or not ? Thanks in advance :)
The output files are explained in the README. Just go here: https://github.com/taoliu/MACS and look near the bottom of the page for the "Output Files" section. The narrowPeak file is an extension of the BED format, which is why it's used for bedtools.
You are going to have be a lot more specific about how you want to "improve macs2 analysis".
If you have basic questions regarding a tool, the tool's manual or website is usually a good place to start. It explains all of the output files of MACS2, including what each field means.
The narrowPeaks format is basically just ENCODE's own BED6+4 format. If you want to intersect output from MACS2, those files are generally the ones to use, as the summit files only give the single base position for each peak where signal is the highest. And the Excel files aren't compatible with bedtools.
A good list of bioinformatics file formats can be found here, it may be useful for you.
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