10f0f6d5160a96867ecf534e1b9d138df7d9b796 lrnassar Mon Sep 28 16:17:46 2026 -0700 Fiber-seq: hide the container by default, and split the five GM lines out into a Rare disease sample class. Max asked for superTrack on rather than on show, since the track covers much the same ground as ENCODE DNase and does not earn a slot in everyone's default hg38 view. The five lymphoblastoid lines GM25455, GM25456, GM27730, GM28570 and GM28572 had been filed as Common Cell Line; Andrew Stergachis says they are rare disease cases consented to broad genomic data sharing and the first of a batch the lab intends to keep adding, so SAMPLE_CLASS_COLORS gains a third entry and the facet now reads 20 HPRC, 16 Common Cell Line, 5 Rare disease sample. refs #36210 diff --git src/hg/makeDb/trackDb/human/hg38/fiberSeqCompendium.html src/hg/makeDb/trackDb/human/hg38/fiberSeqCompendium.html index 8ce5d3b224d..9d222bea464 100644 --- src/hg/makeDb/trackDb/human/hg38/fiberSeqCompendium.html +++ src/hg/makeDb/trackDb/human/hg38/fiberSeqCompendium.html @@ -1,22 +1,22 @@ <h2>Description</h2> <p> This track is part of the <a href="hgTrackUi?db=hg38&g=fiberSeq">Fiber-seq</a> collection. It holds the full Fiber-seq data for 41 samples: 14 cell lines and 27 lymphoblastoid lines, 20 of them from -individuals sequenced by the Human Pangenome Reference Consortium and the rest from ENCODE, the -Genome in a Bottle project and other sources. Chromatin accessibility and CpG methylation are read from the same +individuals sequenced by the Human Pangenome Reference Consortium and five from rare disease +cases. Chromatin accessibility and CpG methylation are read from the same molecules in the same experiment, so both are kept in one table here and can be compared without worrying about differences in cell preparation or sequencing depth. Six kinds of data are available for each sample: </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 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> <li>CpG methylation: percent of reads methylated at each CpG, over both chromosomes.</li> <li>Haplotype CpG: the same measure computed separately for the two parental chromosomes.</li> @@ -77,36 +77,41 @@ <p> 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. </p> <p> The color swatches next to the Sample class filters are: </p> <table class="stdTbl"> <tr><th style="background-color:#0072B2;width:2em"> </th> <td>HPRC, a lymphoblastoid (B-lymphocyte, EBV) line from the Human Pangenome Reference Consortium</td></tr> <tr><th style="background-color:#D55E00;width:2em"> </th> - <td>Common cell line. Seven of these are lymphoblastoid as well but come from elsewhere: - GM12878 from ENCODE, HG002 from the Genome in a Bottle project, and GM25455, GM25456, - GM27730, GM28570 and GM28572. The classification is the one supplied by the - laboratory, not one inferred from the cell type</td></tr> + <td>Common cell line. Two of these are lymphoblastoid as well but come from elsewhere: + GM12878 from ENCODE and HG002 from the Genome in a Bottle project</td></tr> + <tr><th style="background-color:#009E73;width:2em"> </th> + <td>Rare disease sample, from a case consented to broad genomic data sharing. Five so far: + GM25455, GM25456, GM27730, GM28570 and GM28572</td></tr> </table> +<p> +The classification is the one supplied by the laboratory, not one inferred from the cell type. +</p> + <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. The FDR value stops at 100, which is the highest the pipeline reports rather than a real ceiling on significance, and 9 percent of the peaks in this track sit at it; filtering at the top of that range therefore selects a large group rather than a handful of outstanding peaks. 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>