b260fe1f52db8c7e5362d4f9db3770409c24e197 hiram Thu Apr 14 18:57:29 2022 -0700 add the liftOver chainNet tracks refs #29272 diff --git src/hg/makeDb/trackDb/human/chainNetHuman.ra src/hg/makeDb/trackDb/human/chainNetHuman.ra index cfa76b9..96a3375 100644 --- src/hg/makeDb/trackDb/human/chainNetHuman.ra +++ src/hg/makeDb/trackDb/human/chainNetHuman.ra @@ -1,243 +1,312 @@ track humanChainNet compositeTrack on shortLabel Human Chain/Net longLabel Human Genomes, Chain and Net Alignments subGroup1 view Views chain=Chains net=Nets subGroup2 species Species s000=CHM13 s001=HG002_mat s002=HG002_pat subGroup3 clade Clade c00=human dragAndDrop subTracks visibility hide group compGeno noInherit on color 0,0,0 altColor 255,255,0 type bed 3 chainLinearGap loose chainMinScore 5000 dimensions dimensionX=clade dimensionY=species sortOrder species=+ view=+ clade=+ configurable on html homoSapiensChainNet track humanChainNetViewchain shortLabel Chains view chain visibility pack subTrack humanChainNet spectrum on track chainGCA_009914755.4 parent humanChainNetViewchain subGroups view=chain species=s000 clade=c00 shortLabel CHM13 T2T Chain longLabel CHM13 T2T (Jan. 2022 GCA_009914755.4_CHM13_T2T_v2.0) Chained Alignments type bigChain GCA_009914755.4 bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCA_009914755.4.bb linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCA_009914755.4Link.bb otherDb GCA_009914755.4 priority 1 track chainSynGCA_009914755.4 parent humanChainNetViewchain subGroups view=chain species=s000 clade=c00 shortLabel CHM13 T2T Syn Chain longLabel CHM13 T2T (Jan. 2022 GCA_009914755.4_CHM13_T2T_v2.0) Syntenic Chained Alignments type bigChain GCA_009914755.4 bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCA_009914755.4.bb linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCA_009914755.4Link.bb otherDb GCA_009914755.4 priority 2 track chainRBestGCA_009914755.4 parent humanChainNetViewchain subGroups view=chain species=s000 clade=c00 shortLabel CHM13 T2T RBest Chain longLabel CHM13 T2T (Jan. 2022 GCA_009914755.4_CHM13_T2T_v2.0) Reciprocal Best Chained Alignments type bigChain GCA_009914755.4 bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainRBestGCA_009914755.4.bb linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainRBestGCA_009914755.4Link.bb otherDb GCA_009914755.4 priority 3 + track chainLiftOverGCA_009914755.4 + parent humanChainNetViewchain + subGroups view=chain species=s000 clade=c00 + shortLabel CHM13 T2T LiftOver Chain + longLabel CHM13 T2T (Jan. 2022 GCA_009914755.4_CHM13_T2T_v2.0) Lift Over Chained Alignments + type bigChain GCA_009914755.4 + bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainLiftOverGCA_009914755.4.bb + linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainLiftOverGCA_009914755.4Link.bb + otherDb GCA_009914755.4 + priority 4 + track chainGCA_021951015.1 parent humanChainNetViewchain subGroups view=chain species=s001 clade=c00 shortLabel HG002 mat Chain longLabel HG002 mat (Feb. 2022 GCA_021951015.1_HG002.mat.cur.20211005) Chained Alignments type bigChain GCA_021951015.1 bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCA_021951015.1.bb linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCA_021951015.1Link.bb otherDb GCA_021951015.1 priority 5 track chainSynGCA_021951015.1 parent humanChainNetViewchain subGroups view=chain species=s001 clade=c00 shortLabel HG002 mat Syn Chain longLabel HG002 mat (Feb. 2022 GCA_021951015.1_HG002.mat.cur.20211005) Syntenic Chained Alignments type bigChain GCA_021951015.1 bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCA_021951015.1.bb linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCA_021951015.1Link.bb otherDb GCA_021951015.1 priority 6 track chainRBestGCA_021951015.1 parent humanChainNetViewchain subGroups view=chain species=s001 clade=c00 shortLabel HG002 mat RBest Chain longLabel HG002 mat (Feb. 2022 GCA_021951015.1_HG002.mat.cur.20211005) Reciprocal Best Chained Alignments type bigChain GCA_021951015.1 bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainRBestGCA_021951015.1.bb linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainRBestGCA_021951015.1Link.bb otherDb GCA_021951015.1 priority 7 + track chainLiftOverGCA_021951015.1 + parent humanChainNetViewchain + subGroups view=chain species=s001 clade=c00 + shortLabel HG002 mat Lift Over Chain + longLabel HG002 mat (Feb. 2022 GCA_021951015.1_HG002.mat.cur.20211005) Lift Over Chained Alignments + type bigChain GCA_021951015.1 + bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainLiftOverGCA_021951015.1.bb + linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainLiftOverGCA_021951015.1Link.bb + otherDb GCA_021951015.1 + priority 8 + track chainGCA_021950905.1 parent humanChainNetViewchain subGroups view=chain species=s002 clade=c00 shortLabel HG002 pat Chain longLabel HG002 pat (Feb. 2022 GCA_021950905.1_HG002.pat.cur.20211005) Chained Alignments type bigChain GCA_021950905.1 bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCA_021950905.1.bb linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCA_021950905.1Link.bb otherDb GCA_021950905.1 priority 9 track chainSynGCA_021950905.1 parent humanChainNetViewchain subGroups view=chain species=s002 clade=c00 shortLabel HG002 pat Syn Chain longLabel HG002 pat (Feb. 2022 GCA_021950905.1_HG002.pat.cur.20211005) Syntenic Chained Alignments type bigChain GCA_021950905.1 bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCA_021950905.1.bb linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCA_021950905.1Link.bb otherDb GCA_021950905.1 priority 10 track chainRBestGCA_021950905.1 parent humanChainNetViewchain subGroups view=chain species=s002 clade=c00 shortLabel HG002 pat RBest Chain longLabel HG002 pat (Feb. 2022 GCA_021950905.1_HG002.pat.cur.20211005) Reciprocal Best Chained Alignments type bigChain GCA_021950905.1 bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainRBestGCA_021950905.1.bb linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainRBestGCA_021950905.1Link.bb otherDb GCA_021950905.1 priority 11 + track chainLiftOverGCA_021950905.1 + parent humanChainNetViewchain + subGroups view=chain species=s002 clade=c00 + shortLabel HG002 pat Lift Over Chain + longLabel HG002 pat (Feb. 2022 GCA_021950905.1_HG002.pat.cur.20211005) Lift Over Chained Alignments + type bigChain GCA_021950905.1 + bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainLiftOverGCA_021950905.1.bb + linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainLiftOverGCA_021950905.1Link.bb + otherDb GCA_021950905.1 + priority 12 + track humanMafNetViewnet shortLabel Nets view net visibility dense subTrack humanChainNet track netGCA_009914755.4 parent humanMafNetViewnet subGroups view=net species=s000 clade=c00 shortLabel CHM13 T2T Net longLabel CHM13 T2T (Jan. 2022 GCA_009914755.4_CHM13_T2T_v2.0) Net Alignment type bigMaf bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCA_009914755.4.net.bb summary /gbdb/$D/bbi/chainNet/$D.GCA_009914755.4.net.summary.bb speciesOrder GCA_009914755.4 html chainNet otherDb GCA_009914755.4 priority 1 track synNetGCA_009914755.4 parent humanMafNetViewnet subGroups view=net species=s000 clade=c00 shortLabel CHM13 T2T Syn Net longLabel CHM13 T2T (Jan. 2022 GCA_009914755.4_CHM13_T2T_v2.0) Syntenic Net Alignment type bigMaf bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCA_009914755.4.synNet.bb summary /gbdb/$D/bbi/chainNet/$D.GCA_009914755.4.synNet.summary.bb speciesOrder GCA_009914755.4 otherDb GCA_009914755.4 priority 2 track rbestNetGCA_009914755.4 parent humanMafNetViewnet subGroups view=net species=s000 clade=c00 shortLabel CHM13 T2T RBest Net longLabel CHM13 T2T (Jan. 2022 GCA_009914755.4_CHM13_T2T_v2.0) Reciprocal Best Net Alignment type bigMaf bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCA_009914755.4.rbestNet.bb summary /gbdb/$D/bbi/chainNet/$D.GCA_009914755.4.rbestNet.summary.bb speciesOrder GCA_009914755.4 otherDb GCA_009914755.4 priority 3 + track liftOverNetGCA_009914755.4 + parent humanMafNetViewnet + subGroups view=net species=s000 clade=c00 + shortLabel CHM13 T2T liftOverNet + longLabel CHM13 T2T (Jan. 2022 GCA_009914755.4_CHM13_T2T_v2.0) Lift Over Net Alignment + type bigMaf + bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCA_009914755.4.liftOverNet.bb + summary /gbdb/$D/bbi/chainNet/$D.GCA_009914755.4.liftOverNet.summary.bb + speciesOrder GCA_009914755.4 + otherDb GCA_009914755.4 + priority 4 + track netGCA_021951015.1 parent humanMafNetViewnet subGroups view=net species=s001 clade=c00 shortLabel HG002 mat Net longLabel HG002 mat (Feb. 2022 GCA_021951015.1_HG002.mat.cur.20211005) Net Alignment type bigMaf bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCA_021951015.1.net.bb summary /gbdb/$D/bbi/chainNet/$D.GCA_021951015.1.net.summary.bb speciesOrder GCA_021951015.1 html chainNet otherDb GCA_021951015.1 priority 5 track synNetGCA_021951015.1 parent humanMafNetViewnet subGroups view=net species=s001 clade=c00 shortLabel HG002 mat Syn Net longLabel HG002 mat (Feb. 2022 GCA_021951015.1_HG002.mat.cur.20211005) Syntenic Net Alignment type bigMaf bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCA_021951015.1.synNet.bb summary /gbdb/$D/bbi/chainNet/$D.GCA_021951015.1.synNet.summary.bb speciesOrder GCA_021951015.1 otherDb GCA_021951015.1 priority 6 track rbestNetGCA_021951015.1 parent humanMafNetViewnet subGroups view=net species=s001 clade=c00 shortLabel HG002 mat RBest Net longLabel HG002 mat (Feb. 2022 GCA_021951015.1_HG002.mat.cur.20211005) Reciprocal Best Net Alignment type bigMaf bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCA_021951015.1.rbestNet.bb summary /gbdb/$D/bbi/chainNet/$D.GCA_021951015.1.rbestNet.summary.bb speciesOrder GCA_021951015.1 otherDb GCA_021951015.1 priority 7 + track liftOverNetGCA_021951015.1 + parent humanMafNetViewnet + subGroups view=net species=s001 clade=c00 + shortLabel HG002 mat liftOverNet + longLabel HG002 mat (Feb. 2022 GCA_021951015.1_HG002.mat.cur.20211005) Lift Over Net Alignment + type bigMaf + bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCA_021951015.1.liftOverNet.bb + summary /gbdb/$D/bbi/chainNet/$D.GCA_021951015.1.liftOverNet.summary.bb + speciesOrder GCA_021951015.1 + otherDb GCA_021951015.1 + priority 8 + track netGCA_021950905.1 parent humanMafNetViewnet subGroups view=net species=s002 clade=c00 shortLabel HG002 pat Net longLabel HG002 pat (Feb. 2022 GCA_021950905.1_HG002.pat.cur.20211005) Net Alignment type bigMaf bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCA_021950905.1.net.bb summary /gbdb/$D/bbi/chainNet/$D.GCA_021950905.1.net.summary.bb speciesOrder GCA_021950905.1 html chainNet otherDb GCA_021950905.1 priority 9 track synNetGCA_021950905.1 parent humanMafNetViewnet subGroups view=net species=s002 clade=c00 shortLabel HG002 pat Syn Net longLabel HG002 pat (Feb. 2022 GCA_021950905.1_HG002.pat.cur.20211005) Syntenic Net Alignment type bigMaf bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCA_021950905.1.synNet.bb summary /gbdb/$D/bbi/chainNet/$D.GCA_021950905.1.synNet.summary.bb speciesOrder GCA_021950905.1 otherDb GCA_021950905.1 priority 10 track rbestNetGCA_021950905.1 parent humanMafNetViewnet subGroups view=net species=s002 clade=c00 shortLabel HG002 pat RBest Net longLabel HG002 pat (Feb. 2022 GCA_021950905.1_HG002.pat.cur.20211005) Reciprocal Best Net Alignment type bigMaf bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCA_021950905.1.rbestNet.bb summary /gbdb/$D/bbi/chainNet/$D.GCA_021950905.1.rbestNet.summary.bb speciesOrder GCA_021950905.1 otherDb GCA_021950905.1 priority 11 + + track liftOverNetGCA_021950905.1 + parent humanMafNetViewnet + subGroups view=net species=s002 clade=c00 + shortLabel HG002 pat liftOverNet + longLabel HG002 pat (Feb. 2022 GCA_021950905.1_HG002.pat.cur.20211005) Lift Over Net Alignment + type bigMaf + bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCA_021950905.1.liftOverNet.bb + summary /gbdb/$D/bbi/chainNet/$D.GCA_021950905.1.liftOverNet.summary.bb + speciesOrder GCA_021950905.1 + otherDb GCA_021950905.1 + priority 12