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/trackDb.ra src/hg/makeDb/trackDb/human/hg38/trackDb.ra index 00cb3a4c171..c8d03a44b7e 100644 --- src/hg/makeDb/trackDb/human/hg38/trackDb.ra +++ src/hg/makeDb/trackDb/human/hg38/trackDb.ra @@ -939,17 +939,19 @@ include ancient.ra ### initial testing of HPRC chain tracks include hprcV2.trackDb.txt alpha include vgp577way.trackDb.ra alpha include crPred.ra alpha include tad.ra alpha track dnaMethylation override include methbase2.ra alpha +include fiberSeq.ra alpha + include imprinting.ra alpha # include hg38.GCF_040939455.1.chainNet.ra alpha