Hello everyone!
I am analysing a Cut&Run dataset and did peakcalling using MACS2. While looking at file outputs, I got curious if there is any difference between signalValue and FoldEnrichment. The former is a column in .narrowPeak file and latter in .xls peak files. When I compared the column in two files, the values were same. From what I read, there seems is no apparent difference between these two apart from the name. Essentially both denote the average signal intensity at a peak compared to control file.
This is important because I am processing the files for annotation and later on, I plan on filtering out peaks based on average signal intensity/fold enrichment. Since .narrowPeak files are easier to handle with ChIPseeker analyses, I want to process them instead of .xls where I have to do an additional step of converting to Granges format. If there is no inherent difference of calculation between the two, I can confidently proceed to process narrowPeak files for my analysis. So, insights into this will be highly appreciated.
Thank you!
