Hello, I used nfcore/methylseq pipeline to analyze my data and it worked well. My raw data have been obtained by affinity enrichment binding the CpG with Human MBD2A. I got the sorted.markDups_CpG.bedGraph file, that can be successfully imported into IGV. Now, I am in the need to identify:

1. the methylated genes
2. genomic regions (promoter, intronic, exotic, splicing site, TSS)
3. directionality (hypo/hyper methylation) Which application/package (R/python/etc) can be used to import the sorted.markDups_CpG.bedGraph file to retrieve the information I need? Thank you for you support. Emilio