I am trying to use the ROSE algorithm by Young Lab to identify super-enhancers within our novel PRO-seq dataset. I have used dREG to call enhancers from each sample of the PRO-seq dataset and the output is a bed file of identified enhancers. My question is, could I use this bed output as the constituent enhancer file that ROSE requires for the super-enhancer calling? If so, how do I convert this bed file into a gff file for ROSE?
Any help is greatly appreciated!