Frequently Asked Questions

Q: What is bedRMod?

A: The bedRMod format formalizes the ENCODE bedMethyl format to represent RNA modifications.

Q: Why bedRMod?

A: Because standards and guidelines are foundational to open science, data sharing, and reuse; they support sustainable, data-driven method development.

Q: How to work with bedRMod?

A: As you would with BED files. The bedRMod format is generally compatible with the BED format.

Q: What tools produce bedRMod files?

A: So far, only modkit reliably converts modBAM to bedRMod-formatted files out of the box. A number of tools can parse modified base tags from sequence alignments to generate BED-like files, each with its own flavor. This hampers interoperability and limits data reuse across fields.

To use modkit, you need v0.6.1 or higher, and your modBAM file needs a read group tag @RG with a description DS for basecalling and modification models. If you align unmapped modBAM files separately, you may have to re-header them e.g. using samtools addreplacerg. Apart from that, you are completely free to use any modBAM files. You can specify any modification or ChEBI code, if it can’t be inferred from the model names, by using the --modomics-code option.

# example modkit command to generate a bedRMod file
modkit pileup --ref GRCh38_102.fa --modified-bases A:a T:17802 --mod-threshold a:0.95 --mod-threshold 17802:0.99 \
    --bedrmod --organism 9606 --assembly GRCh38 --annotation-source Ensembl --annotation-version 102 \
    --experiment "100_WT_0_IVT_RTA" --external-source "ENA:ERR12772618" \
    dorado_mapped.bam dorado_mapped.bedrmod.gz