01bc05ac9a282a6862111502f13601e513d5b60b max Tue Sep 8 06:16:04 2026 -0700 hg38 Fiber-seq: merge the methylation composite into the compendium The accessibility compendium and the separate Methylation composite covered the identical 41 samples, and cartDump.c assigns priority with the data element as the outer loop and the data type as the inner one. So one composite keeps a sample's six subtracks contiguous in the image, where two composites drew an accessibility block followed by a methylation block and comparing the two assays for one sample meant reading past every other sample. Both come off the same molecules in the same experiment, so side by side is the point. fiberSeqMeth is gone and its three data types moved in as cpg, cpgHap and cpgDiff, renamed because "hap" was already taken by the accessibility overlay and a data type name cannot contain an underscore. Subtracks now carry an explicit priority, sample outer and declared data type inner. Without one they fell back to a label sort, so a first visit showed a sample's data types as Peaks, CpG, Acc rather than in the order of the checkbox row above the table. Metadata columns renamed from camelCase to Accession, Sample_class, _Cell_type and _Sample. toTitleStyle() in facetedComposite.js renders an underscore as a space but does not split camelCase, so "sampleClass" appeared verbatim as a column heading. A literal space cannot be used instead: the saved sort order is a space-separated list of column names and the submit code drops any name containing whitespace, which would have made sorting silently fail to persist. Cell type is no longer faceted. A facet value is only offered when it occurs more than once, and 12 of the 14 cell types here are a single sample, so as a facet it drew two checkboxes and left 12 samples unreachable by any cell-type filter. It is a searchable column now, and Sample_class is the only facet until the lab gives us real HPRC metadata that would facet properly. Description page intro rewritten, and it now says the assay measures the same property as DNase-seq and ATAC-seq. refs #36210 diff --git src/hg/makeDb/trackDb/human/hg38/fiberSeqMeth.html src/hg/makeDb/trackDb/human/hg38/fiberSeqMeth.html deleted file mode 100644 index 0b0f444c8a8..00000000000 --- src/hg/makeDb/trackDb/human/hg38/fiberSeqMeth.html +++ /dev/null @@ -1,154 +0,0 @@ -

Description

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-A methyl group on the cytosine of a CpG dinucleotide is a chemical mark that cells copy along -with the DNA and use to keep genes switched off, most visibly at imprinted genes, where only the -copy inherited from one parent is active, and on the inactive X chromosome. The PacBio instrument -reports native CpG methylation from the same molecules used to measure chromatin accessibility, -so this track and the Fiber-seq Compendium come from -one experiment per sample and can be compared without worrying about differences in cell -preparation or coverage. -

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-For each of the 41 samples three kinds of data are available: -

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-Samples are chosen from a searchable table on this page. Pick the data types along the top, then -select samples in the table. -

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Display Conventions

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-The combined and per-haplotype tracks are drawn 0 to 100 percent methylated with a fixed scale, -using mean as the windowing function, since an average is the meaningful summary for a -methylation level. In the haplotype overlay: -

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 Haplotype 1
 Haplotype 2
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-Which parental chromosome is haplotype 1 is arbitrary and is not consistent between samples. -

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-The haplotype difference track runs from -100 to +100 percent, so a bar above the midline means -haplotype 1 is more methylated and a bar below it means haplotype 2 is. It is a stack of four -overlaid signals, one per significance threshold, drawn least significant first so that the more -significant levels are painted on top: -

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 All measured differences, regardless of significance
 p < 0.01
 p < 0.001
 p < 0.0001
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-The thresholds are nested, so a position drawn red also belongs to all three looser sets. Reading -the track amounts to reading the color: grey is noise, red is a strong difference between the two -chromosomes at that CpG. -

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Methods

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-Permeabilized cells were treated with the Hia5 N6-adenine methyltransferase and sequenced as -PacBio SMRTbell libraries; see the -Fiber-seq Compendium track for the assay details. -The adenine methylation added by the enzyme is chemically distinct from CpG methylation, so both -are read from the same molecule. Base-level CpG methylation was called with jasmine, and the -percent methylation at each genomic position was computed from a pileup of reads using -pb-CpG-tools. Reads were haplotype-phased before the pileup, which gives the per-haplotype -values, and the difference track is the subtraction of one haplotype from the other with the -per-position significance thresholds applied. -

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-The bigWig files were downloaded from -the -Stergachis lab data server, seven files per sample (cpg.combined.bw, -cpg.hap1.bw, cpg.hap2.bw, cpg.diffs_all.bw, -cpg.diffs_p0.01.bw, cpg.diffs_p0.001.bw and cpg.diffs_p0.0001.bw), -and copied to UCSC without modification. The download and integrity steps are documented in the -makeDoc, and the scripts that fetch the data and generate the track -configuration are in the -kent source tree. -

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Data Access

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-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=fiberSeqMeth. -

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-For automated download and analysis, the signal is stored in bigWig files that can be downloaded -from our download -server, one directory per sample accession. The files for this track are the seven named -above. 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/fiberSeq/PM00001/cpg.combined.bw --chrom=chr21 -start=0 -end=100000000 stdout -

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-The mapping from sample accession to sample name and cell type is in -fiberSeqMeth_metadata.tsv. The original data can be downloaded from the -Stergachis -lab data server, and the lab maintains its own track hub and documentation at -fiberseq.github.io. The methylation -pileup tool is at -github.com/PacificBiosciences/pb-CpG-tools. -

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Credits

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-Thanks to Shane Neph, Mitchell Vollger and Andrew Stergachis for generating this data and for -preparing the per-sample methylation hubs that this track was built from. -

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References

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-Vollger MR, Swanson EG, Neph SJ, Ranchalis J, Munson KM, Ho CH, Cheng YHH, Sedeño-Cortés AE, Fondrie -WE, Bohaczuk SC et al. - -A haplotype-resolved view of human gene regulation. -bioRxiv. 2025 Jun 2;. -PMID: 40501892; PMC: PMC12157683 -

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-Stergachis AB, Debo BM, Haugen E, Churchman LS, Stamatoyannopoulos JA. - -Single-molecule regulatory architectures captured by chromatin fiber sequencing. -Science. 2020 Jun 26;368(6498):1449-1454. -PMID: 32587015 -

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