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/fiberSeqCompendium.html src/hg/makeDb/trackDb/human/hg38/fiberSeqCompendium.html new file mode 100644 index 00000000000..37094370614 --- /dev/null +++ src/hg/makeDb/trackDb/human/hg38/fiberSeqCompendium.html @@ -0,0 +1,185 @@ +<h2>Description</h2> + +<p> +This track holds the full Fiber-seq accessibility data for 41 samples: 14 cell lines and 27 +lymphoblastoid lines derived from individuals sequenced by the Human Pangenome Reference +Consortium and the Genome in a Bottle project. For each sample three kinds of data are +available: +</p> + +<ul> + <li>Percent accessible: the fraction of Fiber-seq molecules on which a position was called + accessible, combining both chromosomes.</li> + <li>FIRE peaks: the accessible regulatory elements called from that signal, with a score and + a false discovery rate.</li> + <li>Haplotype accessibility: the same percent-accessible signal computed separately for the + two parental chromosomes and drawn as an overlay, which makes elements that are open on + one chromosome but not the other visible directly.</li> +</ul> + +<p> +Because 41 samples times three data types is too many tracks for a checkbox list, samples are +chosen from a searchable table on this page. Pick the data types you want along the top, then +select samples in the table; the browser turns on that combination for every sample you picked. +The table can be filtered by sample class and cell type, or searched by sample name and +accession. +</p> + +<h2>Display Conventions</h2> + +<p> +Accessibility and haplotype signals are drawn 0 to 100 percent with a fixed scale, so heights +are comparable between samples. The default windowing function is maximum, so a narrow element +survives zooming out. FIRE peaks are shown in dense mode by default, one row per sample. +</p> + +<p> +In the haplotype overlay: +</p> + +<table class="stdTbl"> + <tr><th style="background-color:#0072B2;width:2em"> </th><td>Haplotype 1</td></tr> + <tr><th style="background-color:#D55E00;width:2em"> </th><td>Haplotype 2</td></tr> +</table> + +<p> +The two are overlaid transparently, so a position that is equally accessible on both chromosomes +appears as the two colors superimposed, and a haplotype-selective element appears as one color +standing alone. Which parental chromosome is haplotype 1 is arbitrary and is not consistent +between samples. +</p> + +<p> +The color swatches next to the sample class filters in the table are: +</p> + +<table class="stdTbl"> + <tr><th style="background-color:#0072B2;width:2em"> </th><td>Lymphoblastoid cell line</td></tr> + <tr><th style="background-color:#009E73;width:2em"> </th><td>Stem cell</td></tr> + <tr><th style="background-color:#D55E00;width:2em"> </th><td>Cancer or immortalized cell line</td></tr> +</table> + +<p> +Peaks carry two filterable values, the FIRE score in the signalValue field and the false +discovery rate as a -log10 value in the qValue field, and both can be filtered from a peak +track's own configuration page, along with the score. No filter is applied by default. A short +tick inside each peak marks the point source, the single base the pipeline picked as the summit. +Switching a peak track to pack or full also gives each peak a mouseover with its FIRE score and +FDR; dense mode has no per-peak hover, which is a property of dense display rather than of this +track. The pValue field of the source files is set to -1 throughout and carries no information. +</p> + +<h2>Methods</h2> + +<p> +Permeabilized cells were treated with the Hia5 N6-adenine methyltransferase, which methylates +adenines in DNA not protected by a bound protein, and high molecular weight DNA was prepared +into PacBio SMRTbell libraries and sequenced. Adenine methylation was called with fibertools-rs +v0.4, and reads were aligned and haplotype-phased; for GM12878 an average 20 kb read spans at +least one heterozygous variant and 87.9 percent of reads could be phased against GRCh38. The +FIRE pipeline v0.0.4, a Snakemake workflow, then applied a semi-supervised XGBoost classifier +to label methyltransferase-sensitive patches on each read as FIRE elements. The classifier was +trained with Mokapot over 15 iterations on 21 GM12878 experiments spanning 5.8 to 13.3 percent +adenine methylation, with DNase I and CTCF ChIP-seq peaks as mixed-positive labels. The +aggregate FIRE score at a position is +-50/R times the sum over covering elements of log10(1 - min(EP, 0.99)), where R is the read +depth and EP the estimated precision of each element, which puts the score between 0 and 100; +positions covered by fewer than four FIRE elements are not scored. The false discovery rate was +estimated by shuffling whole reads within a chromosome and comparing the resulting score +distribution to the observed one. Peaks are FIRE score local maxima below a 5 percent FDR with +at least 10 percent of covering reads actuated; adjacent maxima sharing half their elements or +overlapping reciprocally by 90 percent were merged, and peak boundaries were set to the median +start and end of the underlying elements. See Vollger et al. for details. +</p> + +<p> +The bigWig and bigBed 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>, four files per sample +(<tt>all.percent.accessible.bw</tt>, <tt>hap1.percent.accessible.bw</tt>, +<tt>hap2.percent.accessible.bw</tt> and <tt>fire-peaks.bb</tt>). The signal files were copied +without modification. The peak files were rebuilt, because their bigBed header recorded three +data columns while the data has the full ten of a narrowPeak file, which left the browser unable +to see the signalValue and qValue columns for filtering or display. The rebuild corrects the +header and rounds the FIRE score and the FDR to three decimals, which is well beyond the +precision either measure carries. It does drop peaks called on chrEBV, the Epstein-Barr virus decoy of the GRCh38 +analysis set, since that sequence is not part of hg38: 421 of 9,487,043 peaks, in 20 of the 41 +samples, between 2 and 166 peaks each, leaving 9,486,622 in the track. The download, rebuild and +integrity 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 fetch the data and generate the track +configuration are in the +<a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/fiberSeq" +target="_blank">kent source tree</a>. +</p> + +<p> +Two files are empty at the source: the haplotype accessibility bigWigs for GM12878 (accession +PM00001), so its haplotype overlay shows no data. Its combined signal, its peaks and its CpG +methylation are all present, and every other sample has real haplotype files. +</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>fiberSeqCompendium</i>. +</p> + +<p> +For automated download and analysis, the data are stored in bigWig and bigBed files that can be +downloaded from <a href="http://hgdownload.soe.ucsc.edu/gbdb/hg38/fiberSeq/" target="_blank">our +download server</a>, one directory per sample accession. The peak files are called +<tt>fire-peaks.ucsc.bb</tt> and the signal files <tt>all.percent.accessible.bw</tt>, +<tt>hap1.percent.accessible.bw</tt> and <tt>hap2.percent.accessible.bw</tt>. Individual regions +or the whole genome annotation can be obtained using our tools <tt>bigBedToBed</tt> and +<tt>bigWigToBedGraph</tt>, which can be compiled from the source code or downloaded as +precompiled binaries 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 tools can also be used to obtain features within a given range, e.g. +<tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/fiberSeq/PM00001/fire-peaks.ucsc.bb +-chrom=chr21 -start=0 -end=100000000 stdout</tt> +</p> + +<p> +The mapping from sample accession to sample name and cell type is in +<a href="http://hgdownload.soe.ucsc.edu/gbdb/hg38/fiberSeq/fiberSeqCompendium_metadata.tsv" +target="_blank">fiberSeqCompendium_metadata.tsv</a>. 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>. The FIRE pipeline +is at <a href="https://github.com/fiberseq/FIRE" target="_blank">github.com/fiberseq/FIRE</a> and +the methylation caller at +<a href="https://github.com/fiberseq/fibertools-rs" target="_blank">github.com/fiberseq/fibertools-rs</a>. +</p> + +<h2>Credits</h2> + +<p> +Thanks to Mitchell Vollger, Andrew Stergachis and Shane Neph for generating this data, for +assembling it into a track hub and for their help in arranging these tracks for 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> +