ce780dd2f1216ce728ab6bb69ac19a39ddc694fd max Tue Sep 8 00:26:39 2026 -0700 hg38: Fiber-seq container with accessibility, FIRE peaks and CpG methylation, 41 samples Native version of the Stergachis/Vollger lab hub at https://fiberseq.github.io/UCSC-Fiber-seq-hub/hub.txt, plus the per-sample CpG methylation Shane Neph asked to have alongside it. Both cover the same 41 samples: 14 cell lines and 27 lymphoblastoid lines from HPRC and GIAB individuals. fiberSeq container, group regulation fiberSeqAcc multiWig overlay of 7 common cell lines, on by default fiberSeqCompendium faceted composite, dataTypes acc/peaks/hap fiberSeqMeth faceted composite, dataTypes comb/hap/diffs, "Methylation" Both composites use the Methbase faceted-composite machinery. Subtracks are named <composite>_<accession>_<dataType> with the accession as the only middle component, because facetedCompositeUi() cuts the data element at the first underscore and cartDump.c reassembles the name from the pieces; the hub's <composite>_<sample>_<accession>_<type> names would have resolved to tracks that do not exist. Sample name and cell type live in the metadata TSV instead. Using dataTypes also brings onlyVisibility, which is what lets the peaks default to dense while the signal tracks default to full, the mixed-visibility default Andrew Stergachis asked for. 397 GB mirrored from the UW Kopah S3 server rather than pointed at over the network, since a native track should not depend on it. The FIRE peak bigBeds had to be rebuilt: they carry full narrowPeak data but their header records a field count of 3, which hides signalValue and qValue from the browser and would have made hgTracks errAbort in bigNarrowPeakLoadItems(). The rebuild fixes the header and rounds the two float columns to 3 decimals, 467 MB to 313 MB. It drops 421 of 9,487,043 peaks called on chrEBV, the EBV decoy of the GRCh38 analysis set, which hg38 does not have; 9,486,622 remain and every sample reconciles exactly. Reported upstream, along with GM12878's two haplotype accessibility bigWigs, which are one-base placeholders at the source. refs #36210 diff --git src/hg/makeDb/trackDb/human/hg38/fiberSeq.html src/hg/makeDb/trackDb/human/hg38/fiberSeq.html new file mode 100644 index 00000000000..0e8043303cc --- /dev/null +++ src/hg/makeDb/trackDb/human/hg38/fiberSeq.html @@ -0,0 +1,89 @@ +<h2>Description</h2> + +<p> +Most of the DNA in a cell is wrapped around nucleosomes or bound by other proteins, and only +the stretches that are left open can be reached by the transcription factors that switch genes +on. Fiber-seq reads out that protein occupancy directly. Permeabilized cells are treated with +a non-specific N6-adenine methyltransferase, which methylates adenines wherever the DNA is +exposed and leaves protected adenines untouched, so each DNA molecule carries a stencil of the +proteins that were sitting on it. The molecules are then sequenced on a PacBio instrument, +which reports the base sequence, the added adenine methylation and the native CpG methylation +from the same read. Because the reads are long enough to carry heterozygous variants, they can +be assigned to one of the two parental chromosomes, giving a separate picture of chromatin for +each haplotype rather than an average of the two. +</p> + +<p> +This collection holds the Fiber-seq data from the Stergachis and Vollger labs for 41 samples, +covering common cell lines and lymphoblastoid lines from individuals sequenced by the Human +Pangenome Reference Consortium and the Genome in a Bottle project. It contains three tracks: +</p> + +<ul> + <li><a href="hgTrackUi?g=fiberSeqAcc">Fiber-seq Acc</a> shows percent-accessible chromatin + for seven widely used cell lines as a single overlay, so accessibility can be compared + across cell types at a glance.</li> + <li><a href="hgTrackUi?g=fiberSeqCompendium">Fiber-seq Compendium</a> gives, for every one of + the 41 samples, the percent-accessible signal, the called FIRE regulatory element peaks + and a per-haplotype accessibility overlay. Samples are selected from a searchable table.</li> + <li><a href="hgTrackUi?g=fiberSeqMeth">Methylation</a> gives per-sample CpG methylation from + the same reads, both combined over the two chromosomes and split by haplotype, together + with the difference between haplotypes at several significance thresholds.</li> +</ul> + +<p> +Related data can be found in the <a href="hgTrackUi?g=dnaMethylation">DNA Methylation</a> +collection, which holds methylation measured by other assays. +</p> + +<h2>Display Conventions</h2> + +<p> +Each of the three tracks has its own display conventions and its own color scheme; see the +individual track description pages linked above. Signal tracks are scaled 0 to 100 percent +throughout, so a bar height means the same thing in every track and every sample. +</p> + +<h2>Methods</h2> + +<p> +The data were generated and processed by the Stergachis and Vollger labs. Details of the assay, +the machine learning model that calls regulatory elements from single molecules, and the +methylation calling are given on the individual track description pages. +</p> + +<h2>Data Access</h2> + +<p> +The individual track description pages linked above explain how to download the underlying +bigWig and bigBed files and how to query them from scripts. +</p> + +<h2>Credits</h2> + +<p> +Thanks to Mitchell Vollger, Andrew Stergachis and Shane Neph at the University of Washington +and the University of Utah for generating this data, for packaging it for the browser and for +their help in arranging the tracks. +</p> + +<h2>References</h2> + +<p> +Vollger MR, Swanson EG, Neph SJ, Ranchalis J, Munson KM, Ho CH, Cheng YHH, Sedeño-Cortés AE, Fondrie +WE, Bohaczuk SC <em>et al</em>. +<a href="https://www.ncbi.nlm.nih.gov/pubmed/40501892" target="_blank"> +A haplotype-resolved view of human gene regulation</a>. +<em>bioRxiv</em>. 2025 Jun 2;. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/40501892" target="_blank">40501892</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12157683/" target="_blank">PMC12157683</a> +</p> + +<p> +Stergachis AB, Debo BM, Haugen E, Churchman LS, Stamatoyannopoulos JA. +<a href="https://www.ncbi.nlm.nih.gov/pubmed/32587015" target="_blank"> +Single-molecule regulatory architectures captured by chromatin fiber sequencing</a>. +<em>Science</em>. 2020 Jun 26;368(6498):1449-1454. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/32587015" target="_blank">32587015</a> +</p> +