How to Align Dorado BAM with MM Tags Without Losing Methylation Data?

RafaellaSB

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Join Date: Mar 2025

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How to Align Dorado BAM with MM Tags Without Losing Methylation Data?

03-10-2025, 06:02 PM

Hey everyone, I'm working with ONT data and trying to extract methylation calls while keeping the MM tags from Dorado. My workflow is:

Modified basecalling with Dorado (--modified-bases) Produces BAM (with MM tags, but unaligned).
Need to align reads to hg38 with minimap2, but minimap2 only accepts FASTQ.
Extracting FASTQ from BAM loses MM tags, which I need to preserve for methylation analysis.
I found a tool called modbam2bam to realign BAM while keeping MM tags, but I can't find a working download link anywhere.

Does anyone know where I can get modbam2bam, or an alternative approach to align Dorado’s BAM without losing methylation information? Any help is appreciated!
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