Nanopore R9.4.1 HG2 methylation frequencies

This dataset contains the methylation frequencies for the HG2 genome computed using the complete nanopore public dataset available at https://github.com/marbl/CHM13. Nanopore raw signals for 390 Gbp of data (126x 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 gridION data buttery-eel -i min_grid.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_min_grid.fastq --port 5555 --use_tcp basecall promethION data buttery-eel -i prom.blow5 --guppy_bin /install/ont-guppy-6.3.7/bin/ --config dna_r9.4.1_450bps_hac_prom.cfg -x cuda:all -q 7 -o reads_prom.fastq --port 5556 --use_tcp alignment minimap2 -ax map-ont -t40 --secondary=no /genome/hg38noAlt.idx hg2_merged_pass.fastq > hg2_merged_pass.sam samtools sort -@40 -o hg2_merged_pass.bam hg2_merged_pass.sam samtools index hg2_merged_pass.bam methylation calling f5c index -t20 hg2_merged_pass.fastq --skip-slow5-idx --slow5 hg2_merged.blow5 f5c call-methylation -x hpc-low -t20 -g /genome/hg38noAlt.fa -r hg2_merged_pass.fastq -b hg2_merged_pass.bam --slow5 hg2_merged.blow5 > hg2_merged_pass_f5c_meth.tsv f5c meth-freq -s -i hg2_merged_pass_f5c_meth.tsv -o hg2_merged_pass_f5c_methfreq.tsv convert to bigwig tail -n +2 hg2_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 hg2_merged_pass_f5c_methfreq.bigwig