We've been doing a lot of work on Novomethyl and it now has a new mode where it can report % methylation for Cytosine's and it also sports a new run summary that gives some stats on % of cytosine's methylated and the conversion efficiency.
In next week or so well add a new report format that provides a lot more detail than the current BED format report, it will be easily converted to BED format just by selecting required columns.
Linux & Mac OSX versions are available on our download page.
Any feedback or suggestions for improvements are most welcome.
Best Regards, Colin