I am working on epigenetic modifications with aging, especially DNA methylation. I have .bed, .sam and .bedgraph files obtained in bisulfite DNA sequencing.
1) Is there any software other than methylkit for DNA methylation analysis? I am looking for global and chromatin level DNA methylation analysis.
2) Any tool that can analyse CpG methylation level in specif regions e.g promoter region, 5 and 3 UTRs or a specific genes.