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&amp;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">&nbsp;</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">&nbsp;</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">&nbsp;</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>