I'm trying to carry out a differential chromatin accessibility analysis on some ATAC-seq data using DiffBind. The programme requires the .bam file from each replicate, as well as a bed file of previously-called peaks (I used MACS2). The output from MACS2 is a summits.bed file, a peaks.narrowPeak file, and a peaks.xls file. As the analysis calls for a bed file of the peaks, should I be using the previously generated summits.bed file, or should I be reformatting/renaming one of the other two peak files (peaks.narrowPeak or peaks.xls) into a .bed file, and using that instead?
Any advice will be much appreciated!