input regions

[wittney-m]

input regions

[holtjma]

Hello,

You can provide any regions you want to the tool and it will extract those regions accordingly. Given that you don't have defined regions of interest, there are two options I would probably recommend:

1. Attempt to create your own CpG island set - I believe UCSC has guidance on how the model organism sets were created. I do not remember the details, but I believe it looked at CpG density over a window, likely with some other heuristics. As long as you have a reference genome, you should be able to create your own set following that same approach. You may also have other organism-specific filters/approaches to define these that I'm unaware of.
2. Take an agnostic approach
   • You could generate windows/tiles across the whole genome of some fixed size and then give that to methbat profile. These would not necessarily be tied to a genomic feature, but you could process afterwards to find windows/tiles of interest.
   • You could also use segmentation instead via methbat segment. This would just tell you which regions were (un)methylated without pre-defined regions.

Hope this helps!
Matt

[holtjma]

Closing this for now, feel free to re-open if this did not resolve your issue.