bdf448295c10bee74b6baa773f6733ce33171996 markd Thu Oct 1 20:56:37 2026 -0700 Store the ProCapNet minus strand negated, and fix group autoscale. refs #35528 Two of the three problems Jairo found on the composite. The negate control did not work on ProCapNet. Its minus-strand files held positive values and were flipped at display time with trackDb negateValues. The composite's control sets one shared value, which replaced the per-track setting and sent both strands the same way, with no route back to the default short of a cart reset. encode4ProCap was fine because ENCODE publishes its minus strand negative already. So put the sign in the data: proCapNetPredToFixedStep gains --negate, proCapNetPredBuild passes it for the minus strand, and negateValues is gone from the stanzas. The twelve existing files were rewritten rather than rebuilt, since the downloads had been deleted; each was checked against its original for identical nBasesCovered, a mirrored value range and exactly negated values. The originals are kept in previousPred, about 197 GB, until QA is done. Group autoscale on the composite did nothing, which was my error: the multiWig containers and the contribution leaves each carried autoScale on, and the child setting wins. The wiggle settings now live only on the composite. The third, an empty row when both strands of a cell line are deselected, is #38441 and is not fixed here. Note in both makedocs and in the generator that this arrangement only partly works and is expected to become a superTrack of multiWig overlays: under a composite, hgTrackUi lists leaves rather than containers, so an overlay gets no inline config block and leaves an empty row when deselected. diff --git src/hg/makeDb/trackDb/human/hg38/transcriptionStart.ra src/hg/makeDb/trackDb/human/hg38/transcriptionStart.ra index 16fd9f4aa25..c3986df4797 100644 --- src/hg/makeDb/trackDb/human/hg38/transcriptionStart.ra +++ src/hg/makeDb/trackDb/human/hg38/transcriptionStart.ra @@ -1,567 +1,495 @@ # 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 Transcription Initiation (TSS) longLabel Transcription initiation (TSS) group rna track encode4ProCap parent transcriptionStart compositeTrack on type bigWig shortLabel PRO-cap longLabel PRO-cap nascent RNA transcription start sites from ENCODE 4 subGroup1 cellLine Cell_line A673=A673 Caco2=Caco-2 Calu3=Calu3 HUVEC=HUVEC K562=K562 MCF10A=MCF10A subGroup2 dataType Data_type procapPos=PRO-cap_+ procapNeg=PRO-cap_- subGroup3 sampleClass Sample_class Cancer=Cancer Noncancer=Non-cancer dimensions dimensionX=dataType dimensionY=cellLine dimA=sampleClass filterComposite dimA sortOrder cellLine=+ dataType=+ configurable on autoScale group alwaysZero on maxHeightPixels 100:40:8 windowingFunction maximum 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 - windowingFunction maximum color 0,114,178 shortLabel A673 PRO-cap longLabel A673 (ENCSR046BCI) PRO-cap transcription start sites, plus up minus down onlyVisibility full priority 1 track encode4ProCap_A673_procap_pos parent encode4ProCap_A673_procap subGroups cellLine=A673 dataType=procapPos sampleClass=Cancer type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/A673.ENCSR046BCI.pos.bw color 0,114,178 shortLabel A673 PRO-cap + longLabel A673 (ENCSR046BCI) PRO-cap transcription start sites, plus strand track encode4ProCap_A673_procap_neg parent encode4ProCap_A673_procap subGroups cellLine=A673 dataType=procapNeg sampleClass=Cancer type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/A673.ENCSR046BCI.neg.bw color 0,114,178 altColor 0,114,178 shortLabel A673 PRO-cap - longLabel A673 (ENCSR046BCI) 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 - windowingFunction maximum color 213,94,0 shortLabel Caco-2 PRO-cap longLabel Caco-2 (ENCSR100LIJ) PRO-cap transcription start sites, plus up minus down onlyVisibility full priority 2 track encode4ProCap_Caco-2_procap_pos parent encode4ProCap_Caco-2_procap subGroups cellLine=Caco2 dataType=procapPos sampleClass=Cancer type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/Caco-2.ENCSR100LIJ.pos.bw color 213,94,0 shortLabel Caco-2 PRO-cap + longLabel Caco-2 (ENCSR100LIJ) PRO-cap transcription start sites, plus strand track encode4ProCap_Caco-2_procap_neg parent encode4ProCap_Caco-2_procap subGroups cellLine=Caco2 dataType=procapNeg sampleClass=Cancer 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 (ENCSR100LIJ) 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 - windowingFunction maximum color 0,158,115 shortLabel Calu3 PRO-cap longLabel Calu3 (ENCSR935RNW) PRO-cap transcription start sites, plus up minus down onlyVisibility full priority 3 track encode4ProCap_Calu3_procap_pos parent encode4ProCap_Calu3_procap subGroups cellLine=Calu3 dataType=procapPos sampleClass=Cancer type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/Calu3.ENCSR935RNW.pos.bw color 0,158,115 shortLabel Calu3 PRO-cap + longLabel Calu3 (ENCSR935RNW) PRO-cap transcription start sites, plus strand track encode4ProCap_Calu3_procap_neg parent encode4ProCap_Calu3_procap subGroups cellLine=Calu3 dataType=procapNeg sampleClass=Cancer type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/Calu3.ENCSR935RNW.neg.bw color 0,158,115 altColor 0,158,115 shortLabel Calu3 PRO-cap - longLabel Calu3 (ENCSR935RNW) 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 - windowingFunction maximum color 204,121,167 shortLabel HUVEC PRO-cap longLabel HUVEC (ENCSR098LLB) PRO-cap transcription start sites, plus up minus down onlyVisibility full priority 4 track encode4ProCap_HUVEC_procap_pos parent encode4ProCap_HUVEC_procap subGroups cellLine=HUVEC dataType=procapPos sampleClass=Noncancer type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/HUVEC.ENCSR098LLB.pos.bw color 204,121,167 shortLabel HUVEC PRO-cap + longLabel HUVEC (ENCSR098LLB) PRO-cap transcription start sites, plus strand track encode4ProCap_HUVEC_procap_neg parent encode4ProCap_HUVEC_procap subGroups cellLine=HUVEC dataType=procapNeg sampleClass=Noncancer type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/HUVEC.ENCSR098LLB.neg.bw color 204,121,167 altColor 204,121,167 shortLabel HUVEC PRO-cap - longLabel HUVEC (ENCSR098LLB) 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 - windowingFunction maximum color 230,159,0 shortLabel K562 PRO-cap longLabel K562 (ENCSR261KBX) PRO-cap transcription start sites, plus up minus down onlyVisibility full priority 5 track encode4ProCap_K562_procap_pos parent encode4ProCap_K562_procap subGroups cellLine=K562 dataType=procapPos sampleClass=Cancer type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/K562.ENCSR261KBX.pos.bw color 230,159,0 shortLabel K562 PRO-cap + longLabel K562 (ENCSR261KBX) PRO-cap transcription start sites, plus strand track encode4ProCap_K562_procap_neg parent encode4ProCap_K562_procap subGroups cellLine=K562 dataType=procapNeg sampleClass=Cancer type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/K562.ENCSR261KBX.neg.bw color 230,159,0 altColor 230,159,0 shortLabel K562 PRO-cap - longLabel K562 (ENCSR261KBX) 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 - windowingFunction maximum color 86,180,233 shortLabel MCF10A PRO-cap longLabel MCF10A (ENCSR799DGV) PRO-cap transcription start sites, plus up minus down onlyVisibility full priority 6 track encode4ProCap_MCF10A_procap_pos parent encode4ProCap_MCF10A_procap subGroups cellLine=MCF10A dataType=procapPos sampleClass=Noncancer type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/MCF10A.ENCSR799DGV.pos.bw color 86,180,233 shortLabel MCF10A PRO-cap + longLabel MCF10A (ENCSR799DGV) PRO-cap transcription start sites, plus strand track encode4ProCap_MCF10A_procap_neg parent encode4ProCap_MCF10A_procap subGroups cellLine=MCF10A dataType=procapNeg sampleClass=Noncancer type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/MCF10A.ENCSR799DGV.neg.bw color 86,180,233 altColor 86,180,233 shortLabel MCF10A PRO-cap - longLabel MCF10A (ENCSR799DGV) PRO-cap transcription start sites, minus strand track proCapNet parent transcriptionStart compositeTrack on type bigWig shortLabel ProCapNet longLabel ProCapNet predicted PRO-cap subGroup1 cellLine Cell_line A673=A673 Caco2=Caco-2 Calu3=Calu3 HUVEC=HUVEC K562=K562 MCF10A=MCF10A subGroup2 dataType Data_type predPos=Predicted_+ predNeg=Predicted_- contrib=Contribution_scores subGroup3 sampleClass Sample_class Cancer=Cancer Noncancer=Non-cancer dimensions dimensionX=dataType dimensionY=cellLine dimA=sampleClass filterComposite dimA sortOrder cellLine=+ dataType=+ configurable on autoScale group alwaysZero on maxHeightPixels 100:40:8 windowingFunction maximum 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 - windowingFunction maximum color 0,114,178 shortLabel A673 Predicted longLabel A673 (ENCSR072YCM) ProCapNet predicted PRO-cap, plus up minus down onlyVisibility full priority 1 track proCapNet_A673_pred_pos parent proCapNet_A673_pred subGroups cellLine=A673 dataType=predPos sampleClass=Cancer type bigWig bigDataUrl /gbdb/hg38/proCapNet/pred/A673.proCapNet.pos.bw color 0,114,178 shortLabel A673 Predicted + longLabel A673 (ENCSR072YCM) ProCapNet predicted PRO-cap, plus strand track proCapNet_A673_pred_neg parent proCapNet_A673_pred subGroups cellLine=A673 dataType=predNeg sampleClass=Cancer type bigWig bigDataUrl /gbdb/hg38/proCapNet/pred/A673.proCapNet.neg.bw color 0,114,178 altColor 0,114,178 - negateValues on shortLabel A673 Predicted - longLabel A673 (ENCSR072YCM) 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 - windowingFunction maximum color 213,94,0 shortLabel Caco-2 Predicted longLabel Caco-2 (ENCSR182QNJ) ProCapNet predicted PRO-cap, plus up minus down onlyVisibility full priority 2 track proCapNet_Caco-2_pred_pos parent proCapNet_Caco-2_pred subGroups cellLine=Caco2 dataType=predPos sampleClass=Cancer type bigWig bigDataUrl /gbdb/hg38/proCapNet/pred/Caco-2.proCapNet.pos.bw color 213,94,0 shortLabel Caco-2 Predicted + longLabel Caco-2 (ENCSR182QNJ) ProCapNet predicted PRO-cap, plus strand track proCapNet_Caco-2_pred_neg parent proCapNet_Caco-2_pred subGroups cellLine=Caco2 dataType=predNeg sampleClass=Cancer 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 Predicted - longLabel Caco-2 (ENCSR182QNJ) 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 - windowingFunction maximum color 0,158,115 shortLabel Calu3 Predicted longLabel Calu3 (ENCSR797DEF) ProCapNet predicted PRO-cap, plus up minus down onlyVisibility full priority 3 track proCapNet_Calu3_pred_pos parent proCapNet_Calu3_pred subGroups cellLine=Calu3 dataType=predPos sampleClass=Cancer type bigWig bigDataUrl /gbdb/hg38/proCapNet/pred/Calu3.proCapNet.pos.bw color 0,158,115 shortLabel Calu3 Predicted + longLabel Calu3 (ENCSR797DEF) ProCapNet predicted PRO-cap, plus strand track proCapNet_Calu3_pred_neg parent proCapNet_Calu3_pred subGroups cellLine=Calu3 dataType=predNeg sampleClass=Cancer type bigWig bigDataUrl /gbdb/hg38/proCapNet/pred/Calu3.proCapNet.neg.bw color 0,158,115 altColor 0,158,115 - negateValues on shortLabel Calu3 Predicted - longLabel Calu3 (ENCSR797DEF) 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 - windowingFunction maximum color 204,121,167 shortLabel HUVEC Predicted longLabel HUVEC (ENCSR801ECP) ProCapNet predicted PRO-cap, plus up minus down onlyVisibility full priority 4 track proCapNet_HUVEC_pred_pos parent proCapNet_HUVEC_pred subGroups cellLine=HUVEC dataType=predPos sampleClass=Noncancer type bigWig bigDataUrl /gbdb/hg38/proCapNet/pred/HUVEC.proCapNet.pos.bw color 204,121,167 shortLabel HUVEC Predicted + longLabel HUVEC (ENCSR801ECP) ProCapNet predicted PRO-cap, plus strand track proCapNet_HUVEC_pred_neg parent proCapNet_HUVEC_pred subGroups cellLine=HUVEC dataType=predNeg sampleClass=Noncancer type bigWig bigDataUrl /gbdb/hg38/proCapNet/pred/HUVEC.proCapNet.neg.bw color 204,121,167 altColor 204,121,167 - negateValues on shortLabel HUVEC Predicted - longLabel HUVEC (ENCSR801ECP) 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 - windowingFunction maximum color 230,159,0 shortLabel K562 Predicted longLabel K562 (ENCSR740IPL) ProCapNet predicted PRO-cap, plus up minus down onlyVisibility full priority 5 track proCapNet_K562_pred_pos parent proCapNet_K562_pred subGroups cellLine=K562 dataType=predPos sampleClass=Cancer type bigWig bigDataUrl /gbdb/hg38/proCapNet/pred/K562.proCapNet.pos.bw color 230,159,0 shortLabel K562 Predicted + longLabel K562 (ENCSR740IPL) ProCapNet predicted PRO-cap, plus strand track proCapNet_K562_pred_neg parent proCapNet_K562_pred subGroups cellLine=K562 dataType=predNeg sampleClass=Cancer type bigWig bigDataUrl /gbdb/hg38/proCapNet/pred/K562.proCapNet.neg.bw color 230,159,0 altColor 230,159,0 - negateValues on shortLabel K562 Predicted - longLabel K562 (ENCSR740IPL) 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 - windowingFunction maximum color 86,180,233 shortLabel MCF10A Predicted longLabel MCF10A (ENCSR860TYZ) ProCapNet predicted PRO-cap, plus up minus down onlyVisibility full priority 6 track proCapNet_MCF10A_pred_pos parent proCapNet_MCF10A_pred subGroups cellLine=MCF10A dataType=predPos sampleClass=Noncancer type bigWig bigDataUrl /gbdb/hg38/proCapNet/pred/MCF10A.proCapNet.pos.bw color 86,180,233 shortLabel MCF10A Predicted + longLabel MCF10A (ENCSR860TYZ) ProCapNet predicted PRO-cap, plus strand track proCapNet_MCF10A_pred_neg parent proCapNet_MCF10A_pred subGroups cellLine=MCF10A dataType=predNeg sampleClass=Noncancer type bigWig bigDataUrl /gbdb/hg38/proCapNet/pred/MCF10A.proCapNet.neg.bw color 86,180,233 altColor 86,180,233 - negateValues on shortLabel MCF10A Predicted - longLabel MCF10A (ENCSR860TYZ) ProCapNet predicted PRO-cap, minus strand track proCapNet_A673_contrib subGroups cellLine=A673 dataType=contrib sampleClass=Cancer 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 Contribution longLabel A673 (ENCSR072YCM) ProCapNet sequence-contribution scores onlyVisibility full priority 11 track proCapNet_Caco-2_contrib subGroups cellLine=Caco2 dataType=contrib sampleClass=Cancer 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 Contribution longLabel Caco-2 (ENCSR182QNJ) ProCapNet sequence-contribution scores onlyVisibility full priority 12 track proCapNet_Calu3_contrib subGroups cellLine=Calu3 dataType=contrib sampleClass=Cancer 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 Contribution longLabel Calu3 (ENCSR797DEF) ProCapNet sequence-contribution scores onlyVisibility full priority 13 track proCapNet_HUVEC_contrib subGroups cellLine=HUVEC dataType=contrib sampleClass=Noncancer 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 Contribution longLabel HUVEC (ENCSR801ECP) ProCapNet sequence-contribution scores onlyVisibility full priority 14 track proCapNet_K562_contrib subGroups cellLine=K562 dataType=contrib sampleClass=Cancer 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 Contribution longLabel K562 (ENCSR740IPL) ProCapNet sequence-contribution scores onlyVisibility full priority 15 track proCapNet_MCF10A_contrib subGroups cellLine=MCF10A dataType=contrib sampleClass=Noncancer 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 Contribution longLabel MCF10A (ENCSR860TYZ) ProCapNet sequence-contribution scores onlyVisibility full priority 16