Nanopore R9.4.1 NA12878 methylation frequencies

This dataset contains the methylation frequencies for the NA12878 computed using the complete nanopore public dataset available at https://github.com/nanopore-wgs-consortium/NA12878/blob/master/Genome.md. Nanopore raw signals for ~130 Gbp of data (~40x coverage) were downloaded and then converted to BLOW5 format using slow5tools. Then, they were basecalled using buttery-eel under Guppy 6.3.7 high accuracy mode. Reads that passed the qscore filter (>7) were mapped using minimap2 2.17 to hg38noAlt genome. Next, methylation calling was performed using f5c 1.1. Finally, the methylation frequencies output by f5c in tsv format were converted to bigwig format. Commands: basecall #buttery-eel -i na12878_dna_merged.blow5 --guppy_bin /install/ont-guppy-6.3.7/bin/ --config dna_r9.4.1_450bps_hac.cfg -x cuda:all -q 7 -o reads.fastq --port 5555 --use_tcp alignment minimap2 -ax map-ont -t40 --secondary=no /genome/hg38noAlt.idx na12878_dna_merged_pass.fastq > na12878_dna_merged_pass.sam samtools sort -@40 -o na12878_dna_merged_pass.bam na12878_dna_merged_pass.sam samtools index na12878_dna_merged_pass.bam methylation calling f5c index -t20 na12878_dna_merged_pass.fastq --skip-slow5-idx --slow5 na12878_dna_merged.blow5 f5c call-methylation -x hpc-low -t20 -g /genome/hg38noAlt.fa -r na12878_dna_merged_pass.fastq -b na12878_dna_merged_pass.bam --slow5 na12878_dna_merged.blow5 > na12878_dna_merged_pass_f5c_meth.tsv f5c meth-freq -s -i na12878_dna_merged_pass_f5c_meth.tsv -o na12878_dna_merged_pass_f5c_methfreq.tsv convert to bigwig tail -n +2 na12878_dna_merged_pass_f5c_methfreq.tsv | awk '{print $1"\t"$2"\t"$3+1"\t"$7}' | sort -k1,1 -k2,2n > meth_freq.bedgraph bedGraphToBigWig meth_freq.bedgraph /genome/hg38.chrom.sizes na12878_dna_merged_pass_f5c_methfreq.bigwig