Welcome to euf-specs Discussions!

[eboileau]

Current specifications: EU format specifications (bedRMod)

For a rationale, see about EUF

What tools currently produce or handle MM/ML tags?

Oxford Nanopore Technology, e.g. Dorado (Remora, Bonito) write these tags to uBAMs. Modkit is a tool for working with modified bases, e.g. converting the information to bed-like format.

I believe Pacific Biosciences also uses read tags for per-read-base base modifications.

I have seen this, but I have not read the papers, nor tried the tools: modbamtools and modbedtools.

---

To facilitate access to and sharing of high-throughput transcriptome-wide RNA modification data, we need to harmonize data exchange formats. Our aim is to make data as FAIR as possible.