Targeted Methylation Sequencing

[moqri]

Is your feature request related to a problem? Please describe.
I tried to use dnmtools as I always use it (indexing hg38, trim reads, map, methylation count) on a targeted methylation data from ELSA-Seq (e.g. SRR15143251: https://trace.ncbi.nlm.nih.gov/Traces/index.html?view=run_browser&acc=SRR15143251&display=metadata) but the end result was a very small numbers of CpGs (~500) with very low coverage

Describe the solution you'd like
I am not sure what was the cause but to make sure the data is good, I used an another DNAm pipeline and it worked as expected (but much slower of course). I was wondering if dnamtools is meant to work with targeted data. If not, would it be possible to add this feature?

Describe alternatives you've considered
A clear and concise description of any alternative solutions or features you've considered.
If it is expected to work already, is there any changes I need to make to the regular instructions I follow for WGBS?

Thank you for your great tool and I hope it becomes even more popular.