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