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/fiberSeqAcc.html src/hg/makeDb/trackDb/human/hg38/fiberSeqAcc.html new file mode 100644 index 00000000000..610ae63e092 --- /dev/null +++ src/hg/makeDb/trackDb/human/hg38/fiberSeqAcc.html @@ -0,0 +1,122 @@ +<h2>Description</h2> + +<p> +This track shows the fraction of Fiber-seq molecules on which a given position was found to be +accessible, in seven cell lines that are widely used in functional genomics. All seven are drawn +as a single overlay with one color per cell line, so a position that is open in one cell type and +closed in another is easy to spot. Positions where the assay could not decide, because fewer than +four accessible molecules covered them, are left unscored. +</p> + +<p> +For the same signal in all 41 samples, along with called peaks and a per-haplotype breakdown, see +the <a href="hgTrackUi?g=fiberSeqCompendium">Fiber-seq Compendium</a> track. +</p> + +<h2>Display Conventions</h2> + +<p> +The vertical axis is percent of molecules accessible, fixed from 0 to 100, and the seven cell +lines are overlaid transparently in these colors: +</p> + +<table class="stdTbl"> + <tr><th style="background-color:#E69F00;width:2em"> </th><td>GM12878, lymphoblastoid</td></tr> + <tr><th style="background-color:#56B4E9;width:2em"> </th><td>K562, erythroleukemia</td></tr> + <tr><th style="background-color:#009E73;width:2em"> </th><td>HepG2, hepatocyte</td></tr> + <tr><th style="background-color:#F0E442;width:2em"> </th><td>H1, embryonic stem cell</td></tr> + <tr><th style="background-color:#0072B2;width:2em"> </th><td>Hap1, near-haploid myeloid</td></tr> + <tr><th style="background-color:#D55E00;width:2em"> </th><td>Hek293T, embryonic kidney</td></tr> + <tr><th style="background-color:#CC79A7;width:2em"> </th><td>Jurkat, T-lymphocyte</td></tr> +</table> + +<p> +Individual cell lines can be turned on and off, and the graph type and windowing function +changed, on this configuration page. The default windowing function is maximum, so a narrow +accessible element is not averaged away when the view is zoomed out. +</p> + +<h2>Methods</h2> + +<p> +Permeabilized cells were treated with the Hia5 N6-adenine methyltransferase, which methylates +adenines in DNA that is not protected by a bound protein, and high molecular weight DNA was then +prepared into PacBio SMRTbell libraries and sequenced. Adenine methylation was called from the +reads with fibertools-rs, and reads were aligned and haplotype-phased. The FIRE pipeline then +applied a semi-supervised XGBoost classifier to each read to label methyltransferase-sensitive +patches as Fiber-seq Inferred Regulatory Elements (FIRE elements). The classifier was trained on +21 GM12878 experiments spanning 5.8 to 13.3 percent adenine methylation, using DNase I and CTCF +ChIP-seq peaks as positive labels, so that it generalizes across samples with different +methylation efficiency. The percent-accessible value shown here is the number of reads carrying a +FIRE element at a position divided by the number of reads covering it. See Vollger et al. for the +full description. +</p> + +<p> +The bigWig files were downloaded from +<a href="https://s3.kopah.uw.edu/userprod/web/public/hashed.PacBio-Fiber-seq/" target="_blank">the +Stergachis lab data server</a>, one <tt>all.percent.accessible.bw</tt> per sample, and copied to +UCSC without modification. The download and verification steps are documented in the +<a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/fiberSeq.txt" +target="_blank">makeDoc</a>, and the scripts that build the track are in the +<a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/fiberSeq" +target="_blank">kent source tree</a>. +</p> + +<h2>Data Access</h2> + +<p> +The data can be explored interactively in table format with the +<a href="../cgi-bin/hgTables">Table Browser</a> or the +<a href="../cgi-bin/hgIntegrator">Data Integrator</a> and exported from there to spreadsheet or +tab-sep tables. From scripts, the data can be accessed through our +<a href="https://api.genome.ucsc.edu">API</a>, track=<i>fiberSeqAcc</i>. +</p> + +<p> +For automated download and analysis, the signal is stored in bigWig files that can be downloaded +from <a href="http://hgdownload.soe.ucsc.edu/gbdb/hg38/fiberSeq/" target="_blank">our download +server</a>. There is one directory per sample accession, and the file for this track is called +<tt>all.percent.accessible.bw</tt>. Individual regions or the whole genome can be obtained using +our tool <tt>bigWigToBedGraph</tt>, 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 <a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>. The +tool can also be used to obtain values within a given range, e.g. +<tt>bigWigToBedGraph http://hgdownload.soe.ucsc.edu/gbdb/hg38/fiberSeq/PM00001/all.percent.accessible.bw +-chrom=chr21 -start=0 -end=100000000 stdout</tt> +</p> + +<p> +The original data can be downloaded from the +<a href="https://s3.kopah.uw.edu/userprod/web/public/hashed.PacBio-Fiber-seq/" target="_blank">Stergachis +lab data server</a>, and the lab maintains its own track hub and documentation at +<a href="https://fiberseq.github.io/" target="_blank">fiberseq.github.io</a>. +</p> + +<h2>Credits</h2> + +<p> +Thanks to Mitchell Vollger, Andrew Stergachis and Shane Neph for generating this data and for +making it available to the browser. +</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://doi.org/10.1101/2024.06.14.599122" 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> +