Nanopore R9.4.1 CHM13 methylation frequencies

This dataset contains the methylation frequencies for the CHM13 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 chm13_merged_pass.fastq > hg2_merged_pass.sam samtools sort -@40 -o chm13_merged_pass.bam chm13_merged_pass.sam samtools index chm13_merged_pass.bam methylation calling f5c index -t20 chm13_merged_pass.fastq --skip-slow5-idx --slow5 hg2_merged.blow5 f5c call-methylation -x hpc-low -t20 -g /genome/hg38noAlt.fa -r chm13_merged_pass.fastq -b chm13_merged_pass.bam --slow5 chm13_merged.blow5 > hg2_merged_pass_f5c_meth.tsv f5c meth-freq -s -i chm13_merged_pass_f5c_meth.tsv -o chm13_merged_pass_f5c_methfreq.tsv convert to bigwig tail -n +2 chm13_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 chm13_merged_pass_f5c_methfreq.bigwig