MLML, reliable depth

[Humam]

Hi,

First I would like to thank you for the very useful tools you provide!

I have used the updated version of MLML software for the 5hmC estimation, with the new options -M -H for pseudo methcounts outputs.

I would like to inquire if MLML software takes into account a reliable depth number from the BS and oxBS reads? if not what is the cut of that you recommend to use (5x or 10x)?

Besides that, for the the positions with only 1x pseudo count coverage (100% methylation rate), should we keep them in the further analysis?

Many thanks,

Best regards

Humam