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/hg38/transcriptionStart.ra src/hg/makeDb/trackDb/human/hg38/transcriptionStart.ra index f3264ee4a80..c40801e5c20 100644 --- src/hg/makeDb/trackDb/human/hg38/transcriptionStart.ra +++ src/hg/makeDb/trackDb/human/hg38/transcriptionStart.ra @@ -1,517 +1,517 @@ # Generated by hg/makeDb/outside/proCapNet/proCapNetTrackDb for hg38. # 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 encode4ProCap parent transcriptionStart compositeTrack faceted type bigWig shortLabel PRO-cap longLabel PRO-cap nascent RNA transcription start sites from ENCODE 4 metaDataUrl /gbdb/hg38/encode4ProCap/metadata.tsv colorSettingsUrl /gbdb/hg38/encode4ProCap/colors.json primaryKey Cell_line dataTypes procap|"PRO-cap" subtrackUrls Experiment=https://www.encodeproject.org/experiments/$$/ Files=https://hgdownload.soe.ucsc.edu/gbdb/hg38/encode4ProCap/$$ defaultSortField Cell_line maxCheckboxes 50 noInherit on visibility hide priority 1 track encode4ProCap_A673_procap parent encode4ProCap on container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig autoScale on alwaysZero on maxHeightPixels 100:40:8 color 0,114,178 shortLabel A673 PRO-cap longLabel A673 PRO-cap transcription start sites, plus strand up and minus strand down onlyVisibility full priority 1 track encode4ProCap_A673_procap_pos parent encode4ProCap_A673_procap type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/A673.ENCSR046BCI.pos.bw color 0,114,178 shortLabel A673 PRO-cap + longLabel A673 PRO-cap transcription start sites, plus strand track encode4ProCap_A673_procap_neg parent encode4ProCap_A673_procap type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/A673.ENCSR046BCI.neg.bw color 0,114,178 altColor 0,114,178 shortLabel A673 PRO-cap - longLabel A673 PRO-cap transcription start sites, minus strand track encode4ProCap_Caco-2_procap parent encode4ProCap on container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig autoScale on alwaysZero on maxHeightPixels 100:40:8 color 213,94,0 shortLabel Caco-2 PRO-cap longLabel Caco-2 PRO-cap transcription start sites, plus strand up and minus strand down onlyVisibility full priority 2 track encode4ProCap_Caco-2_procap_pos parent encode4ProCap_Caco-2_procap type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/Caco-2.ENCSR100LIJ.pos.bw color 213,94,0 shortLabel Caco-2 PRO-cap + longLabel Caco-2 PRO-cap transcription start sites, plus strand track encode4ProCap_Caco-2_procap_neg parent encode4ProCap_Caco-2_procap type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/Caco-2.ENCSR100LIJ.neg.bw color 213,94,0 altColor 213,94,0 shortLabel Caco-2 PRO-cap - longLabel Caco-2 PRO-cap transcription start sites, minus strand track encode4ProCap_Calu3_procap parent encode4ProCap on container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig autoScale on alwaysZero on maxHeightPixels 100:40:8 color 0,158,115 shortLabel Calu3 PRO-cap longLabel Calu3 PRO-cap transcription start sites, plus strand up and minus strand down onlyVisibility full priority 3 track encode4ProCap_Calu3_procap_pos parent encode4ProCap_Calu3_procap type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/Calu3.ENCSR935RNW.pos.bw color 0,158,115 shortLabel Calu3 PRO-cap + longLabel Calu3 PRO-cap transcription start sites, plus strand track encode4ProCap_Calu3_procap_neg parent encode4ProCap_Calu3_procap type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/Calu3.ENCSR935RNW.neg.bw color 0,158,115 altColor 0,158,115 shortLabel Calu3 PRO-cap - longLabel Calu3 PRO-cap transcription start sites, minus strand track encode4ProCap_HUVEC_procap parent encode4ProCap on container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig autoScale on alwaysZero on maxHeightPixels 100:40:8 color 204,121,167 shortLabel HUVEC PRO-cap longLabel HUVEC PRO-cap transcription start sites, plus strand up and minus strand down onlyVisibility full priority 4 track encode4ProCap_HUVEC_procap_pos parent encode4ProCap_HUVEC_procap type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/HUVEC.ENCSR098LLB.pos.bw color 204,121,167 shortLabel HUVEC PRO-cap + longLabel HUVEC PRO-cap transcription start sites, plus strand track encode4ProCap_HUVEC_procap_neg parent encode4ProCap_HUVEC_procap type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/HUVEC.ENCSR098LLB.neg.bw color 204,121,167 altColor 204,121,167 shortLabel HUVEC PRO-cap - longLabel HUVEC PRO-cap transcription start sites, minus strand track encode4ProCap_K562_procap parent encode4ProCap on container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig autoScale on alwaysZero on maxHeightPixels 100:40:8 color 230,159,0 shortLabel K562 PRO-cap longLabel K562 PRO-cap transcription start sites, plus strand up and minus strand down onlyVisibility full priority 5 track encode4ProCap_K562_procap_pos parent encode4ProCap_K562_procap type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/K562.ENCSR261KBX.pos.bw color 230,159,0 shortLabel K562 PRO-cap + longLabel K562 PRO-cap transcription start sites, plus strand track encode4ProCap_K562_procap_neg parent encode4ProCap_K562_procap type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/K562.ENCSR261KBX.neg.bw color 230,159,0 altColor 230,159,0 shortLabel K562 PRO-cap - longLabel K562 PRO-cap transcription start sites, minus strand track encode4ProCap_MCF10A_procap parent encode4ProCap on container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig autoScale on alwaysZero on maxHeightPixels 100:40:8 color 86,180,233 shortLabel MCF10A PRO-cap longLabel MCF10A PRO-cap transcription start sites, plus strand up and minus strand down onlyVisibility full priority 6 track encode4ProCap_MCF10A_procap_pos parent encode4ProCap_MCF10A_procap type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/MCF10A.ENCSR799DGV.pos.bw color 86,180,233 shortLabel MCF10A PRO-cap + longLabel MCF10A PRO-cap transcription start sites, plus strand track encode4ProCap_MCF10A_procap_neg parent encode4ProCap_MCF10A_procap type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/MCF10A.ENCSR799DGV.neg.bw color 86,180,233 altColor 86,180,233 shortLabel MCF10A PRO-cap - longLabel MCF10A PRO-cap transcription start sites, minus strand track proCapNet parent transcriptionStart compositeTrack faceted type bigWig shortLabel ProCapNet longLabel ProCapNet predicted PRO-cap and sequence-contribution scores metaDataUrl /gbdb/hg38/proCapNet/metadata.tsv colorSettingsUrl /gbdb/hg38/proCapNet/colors.json primaryKey Cell_line dataTypes pred|"Predicted PRO-cap" contrib|"Sequence contribution scores" subtrackUrls Experiment=https://www.encodeproject.org/annotations/$$/ Files=https://hgdownload.soe.ucsc.edu/gbdb/hg38/proCapNet/$$ 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/hg38/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/hg38/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/hg38/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/hg38/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/hg38/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/hg38/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/hg38/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/hg38/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/hg38/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/hg38/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/hg38/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/hg38/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 track proCapNet_A673_contrib parent proCapNet off type bigWig bigDataUrl /gbdb/hg38/proCapNet/contrib/A673.proCapNet-contrib.bw logo on autoScale on alwaysZero on maxHeightPixels 100:40:8 color 0,114,178 shortLabel A673 Contrib longLabel A673 ProCapNet sequence-contribution scores onlyVisibility full priority 11 track proCapNet_Caco-2_contrib parent proCapNet off type bigWig bigDataUrl /gbdb/hg38/proCapNet/contrib/Caco-2.proCapNet-contrib.bw logo on autoScale on alwaysZero on maxHeightPixels 100:40:8 color 213,94,0 shortLabel Caco-2 Contrib longLabel Caco-2 ProCapNet sequence-contribution scores onlyVisibility full priority 12 track proCapNet_Calu3_contrib parent proCapNet off type bigWig bigDataUrl /gbdb/hg38/proCapNet/contrib/Calu3.proCapNet-contrib.bw logo on autoScale on alwaysZero on maxHeightPixels 100:40:8 color 0,158,115 shortLabel Calu3 Contrib longLabel Calu3 ProCapNet sequence-contribution scores onlyVisibility full priority 13 track proCapNet_HUVEC_contrib parent proCapNet off type bigWig bigDataUrl /gbdb/hg38/proCapNet/contrib/HUVEC.proCapNet-contrib.bw logo on autoScale on alwaysZero on maxHeightPixels 100:40:8 color 204,121,167 shortLabel HUVEC Contrib longLabel HUVEC ProCapNet sequence-contribution scores onlyVisibility full priority 14 track proCapNet_K562_contrib parent proCapNet off type bigWig bigDataUrl /gbdb/hg38/proCapNet/contrib/K562.proCapNet-contrib.bw logo on autoScale on alwaysZero on maxHeightPixels 100:40:8 color 230,159,0 shortLabel K562 Contrib longLabel K562 ProCapNet sequence-contribution scores onlyVisibility full priority 15 track proCapNet_MCF10A_contrib parent proCapNet off type bigWig bigDataUrl /gbdb/hg38/proCapNet/contrib/MCF10A.proCapNet-contrib.bw logo on autoScale on alwaysZero on maxHeightPixels 100:40:8 color 86,180,233 shortLabel MCF10A Contrib longLabel MCF10A ProCapNet sequence-contribution scores onlyVisibility full priority 16