DOI: 10.5281/zenodo.10683994
title: A comparison of methods for detecting DNA methylation from long-read sequencing of human genomes.

description: This data is part of a publication in Genome Biology:  A comparison of methods for detecting DNA methylation from long-read sequencing of human genomes, Sigurpálsdóttir et al 2024. 

Data S1: Summary statistics for CpG units averaged over 7,179 samples sequenced using R9.4 flowcell from ONT and methylation called using Nanopolish. Chrom: The chromosome of the CpG unitstart: The nucleotide starting position of the CpG unit, 0 basedend: The nucleotide ending position of the CpG unitn_reliable: The number of realiable reads behind the CpG unit. Reliable is defined as having the absalute log likelihood ratio larger than 1.921n_total: Total number of reads behind the CpG unitratio: The methylation ratio, calculated as number of methylated reliable reads out of all reliable reads.strand_bias: Difference between the methylation ratio of forward and reverse strandFRR: Fraction of reliable reads, calculated as n_reliable/n_totaldark_region: Boolean column indication of whether the CpG unit is within dark region. 1 indicates the CpG unit is within a dark region, 0 indicates it is notSNP: Boolean column indicating whether the CpG unit is within 5bp of SNPphased_frac: Fraction of phased readshq: Boolean column Indicating whether the CpG unit is high-qualityhq_phased: Boolean column indicating whether the CpG unit is high quality with phasing status includedhighSB: Boolean column indicating whether the CpG unit failes on strand bias test and has strand bias greater than 0.2lowFRR: Boolean column indicating if the CpG unit fails on FRR test and has FRR less than 0.5.highCov: Boolean column indicating if the CpG unit fails on coverage test and has coverage greater than 1.5 times the average coveragelowCov: Boolean column indicating if the CpG unit fails on coverage test and has coverage less than 0.5 times the average coveragelowPF: Boolean column indicating if the CpG unit fails on phasing fraction and has PF less than 0.3

 

Data S2: Summary statistics for CpGs averaged over 132 samples sequenced using oxBS.Chrom: The chromosome of the CpGPos: The nucleotide starting position of the CpG, 0 basedN_total: Total number of reads behind the CpGratio: The methylation ratio, calculated as number of methylated reads out of all readsStrand_bias: Difference between the methylation ratio of forward and reverse strand

 

Data S3: Summary statistics for CpGs averaged over 304 samples sequenced using R9.4 flowcell from ONT and methylation called using Guppy.Chrom: The chromosome of CpGstartx: The nucleotide starting position of the CpG, 0 basedend: The nucleotide ending position of the CpGn_total: Total number of reads behind the CpGratio: The methylation ratio, calculated as number of methylated reads out of all reads.strand_bias: Difference between the methylation ratio of forward and reverse stranddark_region: Boolean column indicating if the CpG is within dark region. 1 indicates the CpG unit is within a dark region, 0 indicates it is notSNP: Boolean column indicating if the CpG is within 5bp of SNPhighSB: Boolean column indicating if the CpG failes on strand bias test and has strand bias greater than 0.2highCov: Boolean column indicating if the CpG fails on coverage test and has coverage greater than 1.5 times the average coveragelowCov: Boolean column indicating if the CpG fails on coverage test and has coverage less than 0.5 times the average coveragehq: Boolean column indicating if the CpG is high-quality

 

Data S4: Summary statistics for CpGs, averaged over 22 samples sequenced using R10.4 flowcell from ONT and methylation called using Guppy.Chrom: The chromosome of CpGstartx: The nucleotide starting position of the CpG, 0 basedend: The nucleotide ending position of the CpGn_total: Total number of reads behind the CpGratio: The methylation ratio, calculated as number of methylated reads out of all reads.strand_bias: Difference between the methylation ratio of forward and reverse stranddark_region: Boolean column indicating if the CpG is within dark region. 1 indicates the CpG unit is within a dark region, 0 indicates it is notSNP: Boolean column indicating if the CpG is within 5bp of SNPhighSB: Boolean column indicating if the CpG failes on strand bias test and has strand bias greater than 0.2highCov: Boolean column indicating if the CpG fails on coverage test and has coverage greater than 1.5 times the average coveragelowCov: Boolean column indicating if the CpG fails on coverage test and has coverage less than 0.5 times the average coveragehq: Boolean column indicating if the CpG is high-quality

 

Data S5: Summary statistics for CpGs, averaged over 50 samples sequenced using SMRT-sequencing and methylation called using primrose.Chrom: The chromosome of CpGPos: The nucleotide position of the CpG, 0 basedn_total: Total number of reads behind the CpGratio: The methylation ratio, calculated as number of methylated reads out of all reads.dark_region: Boolean column indicating if the CpG is within dark region. 1 indicates the CpG unit is within a dark region, 0 indicates it is notSNP: Boolean column indicating if the CpG is within 5bp of SNPhighCov: Boolean column indicating if the CpG fails on coverage test and has coverage greater than 1.5 times the average coveragelowCov: Boolean column indicating if the CpG fails on coverage test and has coverage less than 0.5 times the average coveragehq: Boolean column indicating if the CpG is high-quality

 

Data S6: Summary statistics for CpGs, 132 samples sequenced using both oxBS and ONT, filtered on 25x per CpG in oxBS or greater.Chrom: The chromosome of CpGpos_ont: The nucleotide start position of the CpG in ONT data, 0 based

end_ont: The nucleotide end position of the CpG in ONT data, 0 basedratio_ont: The methylation ratio, calculated as number of methylated reads out of all reads in ONT.pos_oxBS: The nucleotide start position of the CpG in oxBS data, 0 basedratio_oxBS: The methylation ratio, calculated as number of methylated reads out of all reads in oxBS.