How is the "fold change over control" bigwig file generated from ATAC-seq data?
I am going through the ENCODE ATAC-seq pipeline and got confused. ENCODE project provides two types of signal BigWig files: fold change over control and signal p-value. They are generated from MACS and bedtools. However, what is the control for ATAC seq? what does the control mean here? I cannot locate it in the pipeline. What command was used to generate them? Please help and thank you in advance!
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