6a173139cd987a0438b9798b902e0f4ba5006062 hiram Thu Feb 9 14:23:02 2023 -0800 adding chainNet definitions for GCF_024166365.1 GCF_018350175.1 GCF_004115215.2 per user request refs #30555 diff --git src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra index e46b1be..4833f44 100644 --- src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra +++ src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra @@ -695,112 +695,306 @@ speciesOrder GCF_000349665.1 speciesLabels GCF_000349665.1="Golden hamster" track rbestNetGCF_000349665.1 parent mafNetGCF_000349665.1iewnet subGroups view=net shortLabel Golden hamster rbestNet longLabel Golden hamster (Mar. 2013 (MesAur1.0/GCF_000349665.1) Reciprocal Best Net Alignment type bigMaf bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_000349665.1.rbestNet.bb summary /gbdb/$D/bbi/chainNet/$D.GCF_000349665.1.rbestNet.summary.bb speciesOrder GCF_000349665.1 speciesLabels GCF_000349665.1="Golden hamster" ############################################################################## -# GCF_024166365.1 - Asiatic elephant - Elephas maximus indicus - taxId: 99487 - mammal +# GCF_024166365.1 - Asiatic elephant - Elephas maximus indicus - taxId: 99487 - mammals ############################################################################## track chainNetGCF_024166365.1 compositeTrack on shortLabel Asiatic elephant Chain/Net -longLabel Asiatic elephant (Jul. 2022 GCF_024166365.1_mEleMax1_primary_haplotyp), Chain and Net Alignments +longLabel Asiatic elephant (Jul. 2022 GCF_024166365.1_mEleMax1 primary haplotype), Chain and Net Alignments subGroup1 view Views chain=Chain net=Net dragAndDrop subTracks visibility hide group compGeno noInherit on priority 100.1 color 0,0,0 altColor 100,50,0 type bed 3 sortOrder view=+ matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91 chainMinScore 3000 chainLinearGap medium matrixHeader A, C, G, T otherDb GCF_024166365.1 html chainNet track chainNetGCF_024166365.1Viewchain shortLabel Chain view chain visibility pack parent chainNetGCF_024166365.1 spectrum on track chainGCF_024166365.1 parent chainNetGCF_024166365.1Viewchain subGroups view=chain shortLabel Asiatic elephant Chain - longLabel Asiatic elephant (Jul. 2022 GCF_024166365.1_mEleMax1_primary_haplotyp) Chained Alignments + longLabel Asiatic elephant (Jul. 2022 GCF_024166365.1_mEleMax1 primary haplotype) Chained Alignments type bigChain GCF_024166365.1 bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCF_024166365.1.bb linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCF_024166365.1Link.bb track chainSynGCF_024166365.1 parent chainNetGCF_024166365.1Viewchain subGroups view=chain - shortLabel Asiatic elephant Chain - longLabel Asiatic elephant (Jul. 2022 GCF_024166365.1_mEleMax1_primary_haplotyp) Syntenic Chained Alignments + shortLabel Asiatic elephant synChain + longLabel Asiatic elephant (Jul. 2022 GCF_024166365.1_mEleMax1 primary haplotype) Syntenic Chained Alignments type bigChain GCF_024166365.1 bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCF_024166365.1.bb linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCF_024166365.1Link.bb track chainRBestGCF_024166365.1 parent chainNetGCF_024166365.1Viewchain subGroups view=chain - shortLabel Asiatic elephant Chain - longLabel Asiatic elephant (Jul. 2022 GCF_024166365.1_mEleMax1_primary_haplotyp) Reciprocal Best Chained Alignments + shortLabel Asiatic elephant rBestChain + longLabel Asiatic elephant (Jul. 2022 GCF_024166365.1_mEleMax1 primary haplotype) Reciprocal Best Chained Alignments type bigChain GCF_024166365.1 bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainRBestGCF_024166365.1.bb linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainRBestGCF_024166365.1Link.bb track mafNetGCF_024166365.1Viewnet shortLabel Net view net visibility full parent chainNetGCF_024166365.1 track netGCF_024166365.1 parent mafNetGCF_024166365.1Viewnet subGroups view=net shortLabel Asiatic elephant mafNet - longLabel Asiatic elephant (Jul. 2022 GCF_024166365.1_mEleMax1_primary_haplotyp) mafNet Alignment + longLabel Asiatic elephant (Jul. 2022 GCF_024166365.1_mEleMax1 primary haplotype) mafNet Alignment type bigMaf bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_024166365.1.net.bb summary /gbdb/$D/bbi/chainNet/$D.GCF_024166365.1.net.summary.bb speciesOrder GCF_024166365.1 speciesLabels GCF_024166365.1="Asiatic elephant" track synNetGCF_024166365.1 parent mafNetGCF_024166365.1Viewnet subGroups view=net - shortLabel Asiatic elephant mafNet - longLabel Asiatic elephant (Jul. 2022 GCF_024166365.1_mEleMax1_primary_haplotyp) Syntenic Net Alignment + shortLabel Asiatic elephant synNet + longLabel Asiatic elephant (Jul. 2022 GCF_024166365.1_mEleMax1 primary haplotype) Syntenic Net Alignment type bigMaf bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_024166365.1.synNet.bb summary /gbdb/$D/bbi/chainNet/$D.GCF_024166365.1.synNet.summary.bb speciesOrder GCF_024166365.1 speciesLabels GCF_024166365.1="Asiatic elephant" track rbestNetGCF_024166365.1 parent mafNetGCF_024166365.1Viewnet subGroups view=net - shortLabel Asiatic elephant mafNet - longLabel Asiatic elephant (Jul. 2022 GCF_024166365.1_mEleMax1_primary_haplotyp) Reciprocal Best Net Alignment + shortLabel Asiatic elephant rBestNet + longLabel Asiatic elephant (Jul. 2022 GCF_024166365.1_mEleMax1 primary haplotype) Reciprocal Best Net Alignment type bigMaf bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_024166365.1.rbestNet.bb summary /gbdb/$D/bbi/chainNet/$D.GCF_024166365.1.rbestNet.summary.bb speciesOrder GCF_024166365.1 speciesLabels GCF_024166365.1="Asiatic elephant" ############################################################################## +# GCF_018350175.1 - domestic cat - Felis catus - taxId: 9685 - mammals +############################################################################## +track chainNetGCF_018350175.1 +compositeTrack on +shortLabel domestic cat Chain/Net +longLabel domestic cat (May 2021 GCF_018350175.1_F.catus_Fca126_mat1.0), Chain and Net Alignments +subGroup1 view Views chain=Chain net=Net +dragAndDrop subTracks +visibility hide +group compGeno +noInherit on +priority 100.1 +color 0,0,0 +altColor 100,50,0 +type bed 3 +sortOrder view=+ +matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91 +chainMinScore 3000 +chainLinearGap medium +matrixHeader A, C, G, T +otherDb GCF_018350175.1 +html chainNet + + track chainNetGCF_018350175.1Viewchain + shortLabel Chain + view chain + visibility pack + parent chainNetGCF_018350175.1 + spectrum on + + track chainGCF_018350175.1 + parent chainNetGCF_018350175.1Viewchain + subGroups view=chain + shortLabel domestic cat Chain + longLabel domestic cat (May 2021 GCF_018350175.1_F.catus_Fca126_mat1.0) Chained Alignments + type bigChain GCF_018350175.1 + bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCF_018350175.1.bb + linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCF_018350175.1Link.bb + + track chainSynGCF_018350175.1 + parent chainNetGCF_018350175.1Viewchain + subGroups view=chain + shortLabel domestic cat synChain + longLabel domestic cat (May 2021 GCF_018350175.1_F.catus_Fca126_mat1.0) Syntenic Chained Alignments + type bigChain GCF_018350175.1 + bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCF_018350175.1.bb + linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCF_018350175.1Link.bb + + track chainRBestGCF_018350175.1 + parent chainNetGCF_018350175.1Viewchain + subGroups view=chain + shortLabel domestic cat rBestChain + longLabel domestic cat (May 2021 GCF_018350175.1_F.catus_Fca126_mat1.0) Reciprocal Best Chained Alignments + type bigChain GCF_018350175.1 + bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainRBestGCF_018350175.1.bb + linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainRBestGCF_018350175.1Link.bb + + track mafNetGCF_018350175.1Viewnet + shortLabel Net + view net + visibility full + parent chainNetGCF_018350175.1 + + track netGCF_018350175.1 + parent mafNetGCF_018350175.1Viewnet + subGroups view=net + shortLabel domestic cat mafNet + longLabel domestic cat (May 2021 GCF_018350175.1_F.catus_Fca126_mat1.0) mafNet Alignment + type bigMaf + bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_018350175.1.net.bb + summary /gbdb/$D/bbi/chainNet/$D.GCF_018350175.1.net.summary.bb + speciesOrder GCF_018350175.1 + speciesLabels GCF_018350175.1="domestic cat" + + track synNetGCF_018350175.1 + parent mafNetGCF_018350175.1Viewnet + subGroups view=net + shortLabel domestic cat synNet + longLabel domestic cat (May 2021 GCF_018350175.1_F.catus_Fca126_mat1.0) Syntenic Net Alignment + type bigMaf + bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_018350175.1.synNet.bb + summary /gbdb/$D/bbi/chainNet/$D.GCF_018350175.1.synNet.summary.bb + speciesOrder GCF_018350175.1 + speciesLabels GCF_018350175.1="domestic cat" + + track rbestNetGCF_018350175.1 + parent mafNetGCF_018350175.1Viewnet + subGroups view=net + shortLabel domestic cat rBestNet + longLabel domestic cat (May 2021 GCF_018350175.1_F.catus_Fca126_mat1.0) Reciprocal Best Net Alignment + type bigMaf + bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_018350175.1.rbestNet.bb + summary /gbdb/$D/bbi/chainNet/$D.GCF_018350175.1.rbestNet.summary.bb + speciesOrder GCF_018350175.1 + speciesLabels GCF_018350175.1="domestic cat" + +############################################################################## +# GCF_004115215.2 - platypus - Ornithorhynchus anatinus - taxId: 9258 - mammals +############################################################################## +track chainNetGCF_004115215.2 +compositeTrack on +shortLabel platypus Chain/Net +longLabel platypus (Nov. 2020 GCF_004115215.2_mOrnAna1.pri.v4), Chain and Net Alignments +subGroup1 view Views chain=Chain net=Net +dragAndDrop subTracks +visibility hide +group compGeno +noInherit on +priority 540.3 +color 0,0,0 +altColor 100,50,0 +type bed 3 +sortOrder view=+ +matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91 +chainMinScore 3000 +chainLinearGap medium +matrixHeader A, C, G, T +otherDb GCF_004115215.2 +html chainNet + + track chainNetGCF_004115215.2Viewchain + shortLabel Chain + view chain + visibility pack + parent chainNetGCF_004115215.2 + spectrum on + + track chainGCF_004115215.2 + parent chainNetGCF_004115215.2Viewchain + subGroups view=chain + shortLabel platypus Chain + longLabel platypus (Nov. 2020 GCF_004115215.2_mOrnAna1.pri.v4) Chained Alignments + type bigChain GCF_004115215.2 + bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCF_004115215.2.bb + linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCF_004115215.2Link.bb + + track chainSynGCF_004115215.2 + parent chainNetGCF_004115215.2Viewchain + subGroups view=chain + shortLabel platypus synChain + longLabel platypus (Nov. 2020 GCF_004115215.2_mOrnAna1.pri.v4) Syntenic Chained Alignments + type bigChain GCF_004115215.2 + bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCF_004115215.2.bb + linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCF_004115215.2Link.bb + + track chainRBestGCF_004115215.2 + parent chainNetGCF_004115215.2Viewchain + subGroups view=chain + shortLabel platypus rBestChain + longLabel platypus (Nov. 2020 GCF_004115215.2_mOrnAna1.pri.v4) Reciprocal Best Chained Alignments + type bigChain GCF_004115215.2 + bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainRBestGCF_004115215.2.bb + linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainRBestGCF_004115215.2Link.bb + + track mafNetGCF_004115215.2Viewnet + shortLabel Net + view net + visibility full + parent chainNetGCF_004115215.2 + + track netGCF_004115215.2 + parent mafNetGCF_004115215.2Viewnet + subGroups view=net + shortLabel platypus mafNet + longLabel platypus (Nov. 2020 GCF_004115215.2_mOrnAna1.pri.v4) mafNet Alignment + type bigMaf + bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_004115215.2.net.bb + summary /gbdb/$D/bbi/chainNet/$D.GCF_004115215.2.net.summary.bb + speciesOrder GCF_004115215.2 + speciesLabels GCF_004115215.2="platypus" + + track synNetGCF_004115215.2 + parent mafNetGCF_004115215.2Viewnet + subGroups view=net + shortLabel platypus synNet + longLabel platypus (Nov. 2020 GCF_004115215.2_mOrnAna1.pri.v4) Syntenic Net Alignment + type bigMaf + bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_004115215.2.synNet.bb + summary /gbdb/$D/bbi/chainNet/$D.GCF_004115215.2.synNet.summary.bb + speciesOrder GCF_004115215.2 + speciesLabels GCF_004115215.2="platypus" + + track rbestNetGCF_004115215.2 + parent mafNetGCF_004115215.2Viewnet + subGroups view=net + shortLabel platypus rBestNet + longLabel platypus (Nov. 2020 GCF_004115215.2_mOrnAna1.pri.v4) Reciprocal Best Net Alignment + type bigMaf + bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_004115215.2.rbestNet.bb + summary /gbdb/$D/bbi/chainNet/$D.GCF_004115215.2.rbestNet.summary.bb + speciesOrder GCF_004115215.2 + speciesLabels GCF_004115215.2="platypus" + +##############################################################################