5e83632c91c1c536880da1e364a41467856135bd markd Tue Sep 22 11:02:32 2026 -0700 Rename the TSS container and trim the ProCapNet description. refs #35528 Both labels on the transcriptionStart container are now "Transcription Initiation (TSS)". Changed in proCapNetTrackDb and the two transcriptionStart.ra files regenerated from it, since they are generated and carry a do-not-edit header. Dropped the Processing at UCSC section from the ProCapNet page. How the files reached UCSC is not something a browser user needs; the makeDoc already records it, including the NaN bases dropped from the hg38 predictions. Replaced the Kundaje lab server link with the ENCODE portal. The six ENCODE records are BPNet-model annotations holding the trained model, contribution scores and predicted signal over a selected region set. The genome-wide predictions in this track are roughly fifty times larger than the ENCODE predicted-signal files and are not part of that release, so the page says so rather than naming ENCODE as their source. Claude-Session: https://claude.ai/code/session_01LAB6jWshLvB7eNXQKWVuW5 diff --git src/hg/makeDb/trackDb/human/hs1/transcriptionStart.ra src/hg/makeDb/trackDb/human/hs1/transcriptionStart.ra index 6962168f2a0..08985bde954 100644 --- src/hg/makeDb/trackDb/human/hs1/transcriptionStart.ra +++ src/hg/makeDb/trackDb/human/hs1/transcriptionStart.ra @@ -1,224 +1,224 @@ # Generated by hg/makeDb/outside/proCapNet/proCapNetTrackDb for hs1. # Do not edit by hand, edit the script and regenerate. track transcriptionStart superTrack on show -shortLabel TSS -longLabel Experimental and computational evidence for transcription start sites (TSS) +shortLabel Transcription Initiation (TSS) +longLabel Transcription Initiation (TSS) group rna track proCapNet parent transcriptionStart compositeTrack faceted type bigWig shortLabel ProCapNet longLabel ProCapNet predicted PRO-cap and sequence-contribution scores metaDataUrl /gbdb/hs1/proCapNet/metadata.tsv colorSettingsUrl /gbdb/hs1/proCapNet/colors.json primaryKey Cell_line dataTypes pred|"Predicted PRO-cap" subtrackUrls Experiment=https://www.encodeproject.org/annotations/$$/ Files=https://hgdownload.soe.ucsc.edu/gbdb/hs1/proCapNet/$$ defaultSortField Cell_line maxCheckboxes 50 noInherit on visibility hide priority 2 track proCapNet_A673_pred parent proCapNet on container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig autoScale on alwaysZero on maxHeightPixels 100:40:8 color 0,114,178 shortLabel A673 Pred longLabel A673 ProCapNet predicted PRO-cap, plus strand up and minus strand down onlyVisibility full priority 1 track proCapNet_A673_pred_pos parent proCapNet_A673_pred type bigWig bigDataUrl /gbdb/hs1/proCapNet/pred/A673.proCapNet.pos.bw color 0,114,178 shortLabel A673 Pred + longLabel A673 ProCapNet predicted PRO-cap, plus strand track proCapNet_A673_pred_neg parent proCapNet_A673_pred type bigWig bigDataUrl /gbdb/hs1/proCapNet/pred/A673.proCapNet.neg.bw color 0,114,178 altColor 0,114,178 negateValues on shortLabel A673 Pred - longLabel A673 ProCapNet predicted PRO-cap, minus strand track proCapNet_Caco-2_pred parent proCapNet on container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig autoScale on alwaysZero on maxHeightPixels 100:40:8 color 213,94,0 shortLabel Caco-2 Pred longLabel Caco-2 ProCapNet predicted PRO-cap, plus strand up and minus strand down onlyVisibility full priority 2 track proCapNet_Caco-2_pred_pos parent proCapNet_Caco-2_pred type bigWig bigDataUrl /gbdb/hs1/proCapNet/pred/Caco-2.proCapNet.pos.bw color 213,94,0 shortLabel Caco-2 Pred + longLabel Caco-2 ProCapNet predicted PRO-cap, plus strand track proCapNet_Caco-2_pred_neg parent proCapNet_Caco-2_pred type bigWig bigDataUrl /gbdb/hs1/proCapNet/pred/Caco-2.proCapNet.neg.bw color 213,94,0 altColor 213,94,0 negateValues on shortLabel Caco-2 Pred - longLabel Caco-2 ProCapNet predicted PRO-cap, minus strand track proCapNet_Calu3_pred parent proCapNet on container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig autoScale on alwaysZero on maxHeightPixels 100:40:8 color 0,158,115 shortLabel Calu3 Pred longLabel Calu3 ProCapNet predicted PRO-cap, plus strand up and minus strand down onlyVisibility full priority 3 track proCapNet_Calu3_pred_pos parent proCapNet_Calu3_pred type bigWig bigDataUrl /gbdb/hs1/proCapNet/pred/Calu3.proCapNet.pos.bw color 0,158,115 shortLabel Calu3 Pred + longLabel Calu3 ProCapNet predicted PRO-cap, plus strand track proCapNet_Calu3_pred_neg parent proCapNet_Calu3_pred type bigWig bigDataUrl /gbdb/hs1/proCapNet/pred/Calu3.proCapNet.neg.bw color 0,158,115 altColor 0,158,115 negateValues on shortLabel Calu3 Pred - longLabel Calu3 ProCapNet predicted PRO-cap, minus strand track proCapNet_HUVEC_pred parent proCapNet on container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig autoScale on alwaysZero on maxHeightPixels 100:40:8 color 204,121,167 shortLabel HUVEC Pred longLabel HUVEC ProCapNet predicted PRO-cap, plus strand up and minus strand down onlyVisibility full priority 4 track proCapNet_HUVEC_pred_pos parent proCapNet_HUVEC_pred type bigWig bigDataUrl /gbdb/hs1/proCapNet/pred/HUVEC.proCapNet.pos.bw color 204,121,167 shortLabel HUVEC Pred + longLabel HUVEC ProCapNet predicted PRO-cap, plus strand track proCapNet_HUVEC_pred_neg parent proCapNet_HUVEC_pred type bigWig bigDataUrl /gbdb/hs1/proCapNet/pred/HUVEC.proCapNet.neg.bw color 204,121,167 altColor 204,121,167 negateValues on shortLabel HUVEC Pred - longLabel HUVEC ProCapNet predicted PRO-cap, minus strand track proCapNet_K562_pred parent proCapNet on container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig autoScale on alwaysZero on maxHeightPixels 100:40:8 color 230,159,0 shortLabel K562 Pred longLabel K562 ProCapNet predicted PRO-cap, plus strand up and minus strand down onlyVisibility full priority 5 track proCapNet_K562_pred_pos parent proCapNet_K562_pred type bigWig bigDataUrl /gbdb/hs1/proCapNet/pred/K562.proCapNet.pos.bw color 230,159,0 shortLabel K562 Pred + longLabel K562 ProCapNet predicted PRO-cap, plus strand track proCapNet_K562_pred_neg parent proCapNet_K562_pred type bigWig bigDataUrl /gbdb/hs1/proCapNet/pred/K562.proCapNet.neg.bw color 230,159,0 altColor 230,159,0 negateValues on shortLabel K562 Pred - longLabel K562 ProCapNet predicted PRO-cap, minus strand track proCapNet_MCF10A_pred parent proCapNet on container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig autoScale on alwaysZero on maxHeightPixels 100:40:8 color 86,180,233 shortLabel MCF10A Pred longLabel MCF10A ProCapNet predicted PRO-cap, plus strand up and minus strand down onlyVisibility full priority 6 track proCapNet_MCF10A_pred_pos parent proCapNet_MCF10A_pred type bigWig bigDataUrl /gbdb/hs1/proCapNet/pred/MCF10A.proCapNet.pos.bw color 86,180,233 shortLabel MCF10A Pred + longLabel MCF10A ProCapNet predicted PRO-cap, plus strand track proCapNet_MCF10A_pred_neg parent proCapNet_MCF10A_pred type bigWig bigDataUrl /gbdb/hs1/proCapNet/pred/MCF10A.proCapNet.neg.bw color 86,180,233 altColor 86,180,233 negateValues on shortLabel MCF10A Pred - longLabel MCF10A ProCapNet predicted PRO-cap, minus strand