Part of the Imprinting track collection, this track shows the methylation difference between the maternal and the paternal haplotype at individual CpG sites that were found to be differentially methylated (DMCs). The sites come from 123 trio-phased assemblies of the HPRC release 2. Positive values mean that the maternal copy is more methylated, negative values that the paternal copy is more methylated. The regions in the HPRC2 DMRs track are built from these sites.
The authors calculated the values on the CHM13v2.0 reference. They were lifted to hg38 for this track, see Methods for details.
The track is a bar graph with one value per CpG site. Bars above the zero line (red) show higher methylation on the maternal haplotype and bars below it (blue) higher methylation on the paternal haplotype. When zoomed out, the maximum of all sites in a pixel is shown.
Methylation was called from Oxford Nanopore reads with modkit v0.4.1 and the reads were aligned to the personalized assemblies with Winnowmap v2.03 (-x map-ont -I 8G --MD --cs -y -a -Y -L --eqx), keeping primary alignments. Each diploid assembly was split by haplotype and chain files from haplotype to CHM13v2.0 were built with a Nextflow pipeline running nf-LO and minimap2. Methylation calls were lifted to CHM13v2.0 with CrossMap v0.7.0, using a shift of 1 bp on the negative strand so that the methylation tag stays on the C of the CpG. Maternal and paternal groups were compared per chromosome with DSS v2.58.0 in R v4.5.3, using DSS::DMLtest with smoothing (span 500 bp) and unequal dispersion. Differentially methylated CpGs were called with delta 0 and a p-value below 0.001. See Lucas et al. for details on the HPRC data.
The data file was provided by the authors, who also lifted the values from CHM13v2.0 to hg38 with the chain files of the CHM13 project. The bigWig file was linked into /gbdb without changes, see the makeDoc file.
The data can be explored interactively in table format with the Table Browser or the Data Integrator and exported from there to spreadsheet or tab-sep tables. From scripts, the data can be accessed through our API, track=hprcDmc.
For automated download and analysis, the data is stored in a bigWig file that can be downloaded from our download server. The file for this track is called hprcDmc.bw. Individual regions or the whole genome can be obtained using our tool bigWigToBedGraph, which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain values within a given range, e.g. bigWigToBedGraph http://hgdownload.soe.ucsc.edu/gbdb/hg38/imprinting/hprcImprint/hprcDmc.bw -chrom=chr21 -start=0 -end=100000000 stdout
The original annotation source data was provided by the authors and is available on request.
Thanks to Juhyun Kim and Brandon D. Pickett for providing this track.
Lucas JK, Hebbar P, Liao WW, Macias-Velasco JF, Novak AM, Asri M, Balacco JR, Blair AP, Bolognini D, Ebler J et al. HPRC2: A human pangenome reference with near-complete coverage of common genetic variation. bioRxiv. 2026 Jul 22;. PMID: 42539208; PMC: PMC13419748
Feng H, Wu H. Differential methylation analysis for bisulfite sequencing using DSS. Quant Biol. 2019 Dec 31;7(4):327-334. PMID: 34084562; PMC: PMC8171293
Talenti A, Prendergast J. nf-LO: A Scalable, Containerized Workflow for Genome-to-Genome Lift Over. Genome Biol Evol. 2021 Sep 1;13(9). PMID: 34383887; PMC: PMC8412297
Zhao H, Sun Z, Wang J, Huang H, Kocher JP, Wang L. CrossMap: a versatile tool for coordinate conversion between genome assemblies. Bioinformatics. 2014 Apr 1;30(7):1006-7. PMID: 24351709; PMC: PMC3967108