0db15879749b6753035c8f365e9d69b5987f4c79 lrnassar Tue Feb 17 16:33:46 2026 -0800 Adding assembly specific filters, and updating the track desc page based on author feedback, refs #36264 diff --git src/hg/makeDb/trackDb/sacCer/trackDb.ra src/hg/makeDb/trackDb/sacCer/trackDb.ra index 5aed260e6e7..fa51bd87003 100644 --- src/hg/makeDb/trackDb/sacCer/trackDb.ra +++ src/hg/makeDb/trackDb/sacCer/trackDb.ra @@ -1,238 +1,241 @@ track sgdClone priority 14 shortLabel WashU Clones longLabel Washington University Clones group map visibility hide altColor 180,180,180 type bed 4 + track sgdGene shortLabel SGD Genes longLabel Protein-Coding Genes from Saccharomyces Genome Database group genes priority 39 visibility pack color 0,100,180 type genePred sgdPep hgGene on hgsid on directUrl /cgi-bin/hgGene?hgg_gene=%s&hgg_chrom=%s&hgg_start=%d&hgg_end=%d&hgg_type=%s&db=%s exonArrows on track sgdOther shortLabel SGD Other longLabel Other Features from Saccharomyces Genome Database group genes priority 39.1 visibility pack color 30,130,210 type bed 6 + exonArrows on track mrna override shortLabel S. cer. mRNAs spectrum on intronGap 30 track est override shortLabel S. cer. ESTs track transRegCode shortLabel Regulatory Code longLabel Transcriptional Regulatory Code from Harbison Gordon et al. group regulation priority 92.5 visibility pack spectrum on scoreFilter 500 scoreFilterLimits 200:1000 type bed 5 + exonArrows off track transRegCodeProbe shortLabel Reg. ChIP-chip longLabel ChIP-chip Results from Harbison Gordon et al. group regulation priority 92.6 visibility hide type bed 4 + exonArrows off searchTable transRegCodeProbe searchType bed searchPriority 20 track nucleosome shortLabel Nucleosome longLabel Per base Probability of Nucleasome Occupancy E. Segal et al. group regulation priority 100 visibility full autoScale Off maxHeightPixels 128:36:16 graphTypeDefault Bar gridDefault OFF windowingFunction Mean color 0,0,0 altColor 128,128,128 viewLimits 0:1 spanList 1 type wig 0 100 track nucleosomeStable shortLabel Stable Nucleosomes longLabel Highly Stable Nucleasomes p > 0.5 from Eran Segal (score >= 500) group regulation priority 101 visibility hide scoreFilter 500 spectrum on type bed 5 + exonArrows off track nucleosomeBest shortLabel Best Nucleosomes longLabel Genome wide Single Best Nucleasomes from Eran Segal group regulation priority 102 visibility hide spectrum on type bed 5 + exonArrows off track multizYeast shortLabel Conservation longLabel Seven Species of Saccharomyces, Alignments & Conservation group compGeno priority 100 visibility pack type wigMaf 0.0 1.0 maxHeightPixels 100:40:11 wiggle phastCons yLineOnOff Off autoScale Off pairwise pwMaf speciesOrder sacPar sacMik sacKud sacBay sacCas sacKlu track phastConsElements override longLabel PhastCons Conserved Elements (Seven Species of Saccharomyces) track sevenWayPaper shortLabel Conservation (Std.) longLabel Seven Species of Saccharomyces, Alignments & Standardized Conservation group compGeno priority 105.1 visibility hide type wigMaf 0.0 1.0 maxHeightPixels 100:40:11 wiggle phastConsPaper yLineOnOff Off autoScale Off pairwise pwMaf speciesOrder sacPar sacMik sacKud sacBay sacCas sacKlu searchTable sgdGene searchType sgdGene searchPriority 1 searchTable sgdOther searchType bed searchPriority 20 track uwFootprints compositeTrack on shortLabel UW Footprints longLabel UW Protein/DNA Interaction Footprints group regulation priority 130 type bed 3 noInherit on configurable on subGroup1 view Views Counts=Tag_Counts Map=Mappability Print=Footprints dragAndDrop subTracks track uwFootprintsViewCounts shortLabel Tag Counts view Counts visibility full parent uwFootprints track uwFootprintsTagCounts parent uwFootprintsViewCounts subGroups view=Counts shortLabel Tag Counts longLabel UW Footprints Tag Counts type wig 1 13798 viewLimits 1:146 autoScale Off color 25,25,150 group regulation priority 1 html uwFootprints track uwFootprintsViewMap shortLabel Mappability view Map visibility dense parent uwFootprints track uwFootprintsMappability parent uwFootprintsViewMap subGroups view=Map shortLabel Mappability longLabel UW Footprints Mappability type bed 3 color 25,25,150 group regulation priority 2 html uwFootprints track uwFootprintsViewPrint shortLabel Footprints view Print visibility pack parent uwFootprints track uwFootprintsPrints parent uwFootprintsViewPrint subGroups view=Print shortLabel Footprints longLabel UW Protein-binding Footprints type bed 4 color 25,25,150 group regulation priority 3 html uwFootprints searchTable ensGene searchType genePred semiShortCircuit 1 termRegex [a-z0-9]+[_a-z0-9()-]+(\.[0-9]+)? searchPriority 50 searchName ensGeneGtpGene searchTable ensGene searchType genePred searchMethod prefix semiShortCircuit 1 xrefTable ensGtp xrefQuery select transcript,gene from %s where gene like '%s%%' termRegex [a-z0-9]+[_a-z0-9()-]+(\.[0-9]+)? searchPriority 50 searchName ensDotPrefix searchTable ensGene query select chrom,txStart,txEnd,name from %s where name like '%s.%%' semiShortCircuit 1 termRegex [a-z0-9]+[_a-z0-9()-]+(\.[0-9]+)? searchPriority 50 searchName ensGeneGtpProtein searchTable ensGene searchType genePred searchMethod prefix semiShortCircuit 1 xrefTable ensGtp xrefQuery select transcript,protein from %s where protein like '%s%%' termRegex [QY][a-z0-9-]+(\.[0-9]+)? + +track jaspar2026 override +filterValues.TFName ABF1,ABF2,ACA1,ACE2,ADR1,AFT1,AFT2,ARG80,ARG81,ARO80,ARR1,ASG1,ASH1,AZF1,BAS1,CAD1,CAT8,CBF1,CEP3,CHA4,CIN5,cre-1,CRZ1,CST6,CUP2,CUP9,DAL80,DAL81,DAL82,DOT6,ECM22,ECM23,EDS1,ERT1,fep1,FHL1,FKH1,FKH2,FZF1,GAL4,GAT1,GAT3,GAT4,GCN4,GCR1,GCR2,GIS1,GLN3,GSM1,GZF3,HAC1,HAL9,HAP1,HAP2,HAP3,HAP5,HCM1,HMRA1,HMRA2,HSF1,IME1,INO2,INO4,IXR1,LEU3,loz1,LYS14,MAC1,MATALPHA2,MBP1,MBP1::SWI6,MCM1,MET28,MET31,MET32,MGA1,MIG1,MIG2,MIG3,MOT2,MOT3,msn-1,MSN2,MSN4,NCU00019,NCU02182,NDT80,NHP10,nit-4,NRG1,NSI1,nuc-1,OAF1,OPI1,pcr1,PDR1,PDR3,PDR8,PHD1,PHO2,PHO4,PIP2,PPR1,prz1,PUT3,RAP1,RDR1,RDS1,RDS2,REB1,REI1,RFX1,RGM1,RGT1,RIM101,RLM1,RME1,ROX1,RPH1,RPN4,RSC3,RSC30,rst2,RTG1,RTG3,sak1,SDD4,SFL1,SFP1,SIP4,SKN7,SKO1,SMP1,SNT2,SOK2,SPT15,SPT2,SPT23,SRD1,STB3,STB4,STB5,ste11,STE12,STP1,STP2,STP3,STP4,SUM1,SUT1,SUT2,SWI4,SWI5,TBF1,TBS1,TDA9,TEA1,TEC1,THI2,TOD6,toe1,TOS8,TYE7,UGA3,UME6,UPC2,URC2,USV1,wc-1,XBP1,YAP1,YAP3,YAP5,YAP6,YAP7,YER130C,YER184C,YGR067C,YHP1,YKL222C,YLL054C,YLR278C,YNR063W,YOX1,YPR013C,YPR015C,YPR022C,YPR196W,YRM1,YRR1,ZAP1,zas1,ZMS1