I was wondering if it was possible to convert/collapse bedgraph format files to BED format. I wish to create venn diagrams for chip-seq data.
For my 1st dataset after running MACS, I get both BED and Bedgraph format data (i changed option to get bedgraph instead of wig). However, for my 2nd dataset I only have the data in BED format.
The bedgraph files look nice for visualization on ucsc genome browser because it shows peaks but the R package ChIPpeakAnno requires BED files.