HG002-HG004 R9 methylation basecalled data

The resulting BAM files were merged using samtools with command “samtools merge -l ${bam_list.txt} -o ${merged.bam}”.

The merged BAM file was aligned to the GRCh38 reference genome (GenBank assembly ID GCA_000001405.15) using dorado v0.9.5 (github.com/nanoporetech/dorado) with command “dorado align -t 80 --mm2-opts "-x map-ont" ${reference.fa} > ${output.bam}”, followed by sorting and indexing with Samtools.It should be noted that for datasets basecalled with Guppy v4.2.2 contained “Mm” and “Ml” tags instead of the standard “MM” and “ML” were presented in output BAM file.