66fafe88184bb3a8a45a50026f4d6c7fbbc24109 markd Tue Sep 29 10:12:53 2026 -0700 Rebuild the TSS tracks as traditional composites, for wiggle control. refs #35528 A faceted composite is routed to facetedCompositeUi(), which returns before cfgByCfgType(), so it never draws the wiggle controls: no data view scaling, no viewing range, no windowing function, no track height. Signal tracks need those, so proCapNet and encode4ProCap are now traditional composites. They stay separate composites under the TSS container. The multiWig strand overlays survive the change. The old comment here claimed a multiWig under a plain composite "is flattened away and never drawn"; that is wrong for drawing, which #36320 fixed. Only the hgTrackUi subtrack list flattens, because compositeUiSubtracks() walks to leaves, so the overlays get no inline config block and are configured from their own pages. Raised as #38441. The matrix has to be declared over the leaves, since that is the level hgTrackDb checks: declaring it on the containers fails -strict with "has groups not defined in parent". So a strand is a matrix cell, and the containers carry no subGroups. Sample class survives as a filterComposite dimension, replacing the facet. configurable on gives each subtrack its own config namespace. Drop the faceted machinery: the metadata table, the color file, the constants feeding them and the gbdbDir argument, 39 lines. The metadata.tsv and colors.json already written under /gbdb are now unreferenced and can be deleted. Put the ENCODE accession in each subtrack longLabel, and add a linked table of them to both description pages. A longLabel cannot carry a link, since printSubtrackTableBody() htmlEncodes it, hence the table. The label wording is shortened to keep the longest at 74 characters. diff --git src/hg/makeDb/trackDb/human/encode4ProCap.html src/hg/makeDb/trackDb/human/encode4ProCap.html index e6831ba0819..8cdb28e0b59 100644 --- src/hg/makeDb/trackDb/human/encode4ProCap.html +++ src/hg/makeDb/trackDb/human/encode4ProCap.html @@ -9,73 +9,85 @@ read reports the exact base and strand of one initiation event. Unlike RNA-seq or CAGE, PRO-cap sees unstable RNAs as well as stable ones, which makes initiation at enhancers visible.

This track shows PRO-cap signal from six ENCODE 4 experiments, one per cell line, on GRCh38/hg38 only. The predictions a deep learning model makes from sequence alone, trained on this same data, are in the ProCapNet track, available on GRCh38/hg38 and T2T-CHM13/hs1.

Display Conventions and Configuration

-Cell lines are listed in the table on this page, one row each. Use the Sample -class facet to narrow the list, and the Experiment column to open the experiment -on the ENCODE portal. +The matrix on this page has one row per cell line and one column per strand, so a +checkbox turns on one strand of one cell line. Use the Sample class filter +to restrict the matrix to cancer or non-cancer lines.

Each track is an overlay of the two strands: plus strand reads are drawn upward and minus strand reads downward. The y axis is the number of initiation events measured at that base, summed over the experiment's replicates, so tracks with deeper sequencing reach higher values. Tracks are colored by cell line:

+

+The six experiments, each linking to its record on the ENCODE portal. +

+ + + + + + + + + +
Cell lineTissueSample classENCODE experiment
A673MuscleCancerENCSR046BCI
Caco-2ColonCancerENCSR100LIJ
Calu3LungCancerENCSR935RNW
HUVECBlood vesselNon-cancerENCSR098LLB
K562BloodCancerENCSR261KBX
MCF10ABreastNon-cancerENCSR799DGV
+

Methods

PRO-cap, in the CoPRO form of Tome et al., 2018, runs a nuclear run-on reaction with biotinylated NTPs, captures the biotinylated nascent RNAs, selects for a 5' cap so that only transcripts carrying their original start are kept, and sequences them paired-end. The 5' end of the second read marks the base at which transcription started and its strand gives the strand of initiation. The six experiments were produced by the Yu and Lis labs at Cornell University as part of the ENCODE 4 nascent transcriptome survey described in Shah et al., 2026, and processed through the ENCODE PRO-cap pipeline.

The signal files were downloaded from the ENCODE portal, taking only the plus and minus strand signal of unique reads belonging to each experiment's default analysis. ENCODE publishes no pooled file, so the per-replicate files were summed at UCSC into one track per cell line and strand, the same merge the ProCapNet models were trained on. Total signal is conserved -exactly by the summing, and minus strand signal is negative as released. The -experiments are ENCSR046BCI, ENCSR100LIJ, ENCSR935RNW, ENCSR098LLB, ENCSR261KBX -and ENCSR799DGV for A673, Caco-2, Calu3, HUVEC, K562 and MCF10A respectively. +exactly by the summing, and minus strand signal is negative as released.

The steps are recorded in doc/hg38/transcriptionStart.txt, the scripts are in makeDb/outside/proCapNet, including proCapNetEncodeFiles.tsv, which records exactly which ENCODE file accessions went into each track, and the track configuration is in trackDb/human/hg38/transcriptionStart.ra.

Data Access