Inquiry

[olaraym]

Hello @phue

I find this pipeline and package very useful for the work I am doing currently, thanks for this work. I was wondering if this pipeline can be adapted to long-read (Pacbio and nanopore reads) methylation data, I will be glad to hear your opinion on this. Thanks.

[phue]

Hi @olaraym , Glad you find it useful for your research.

MethylScore was designed for short reads, but I don't see a reason why it would not work with long reads as well. It is possible to supply bedGraph files with per-cytosine information to the pipeline, so if you produce such files with available tools (e.g modkit for nanopore modified basecalling) and convert to bedGraph, it should work.

bismark also gained support for long reads recently, useful for EMseq experiments. bismark produces bedGraph output that is compatible with MethylScore as is.

[olaraym]

Thanks @phue

I will explore that and give you feedback