744eb91b7ac3b786d58b9dad166ce47d6d12273a hiram Fri Apr 10 11:30:52 2020 -0700 adding canFam4 chainNet definitions refs #25279 diff --git src/hg/makeDb/trackDb/trackDb.chainNet.mammal.ra src/hg/makeDb/trackDb/trackDb.chainNet.mammal.ra index b331a51..5b2499e 100644 --- src/hg/makeDb/trackDb/trackDb.chainNet.mammal.ra +++ src/hg/makeDb/trackDb/trackDb.chainNet.mammal.ra @@ -310,15 +310,231 @@ html chainNet track chainNetCriGriChoV2Viewnet shortLabel Net view net visibility full parent chainNetCriGriChoV2 track netCriGriChoV2 parent chainNetCriGriChoV2Viewnet subGroups view=net shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net type netAlign criGriChoV2 chainCriGriChoV2 html chainNet + +################################################################ +# canFam4 - dog - Canis lupus familiaris - mammal - 9615 +# German shepard 'Mischka' +################################################################ +track chainNetCanFam4 +compositeTrack on +shortLabel $o_Organism Chain/Net +longLabel $o_Organism ($o_date), Chain and Net Alignments +subGroup1 view Views chain=Chain net=Net +dragAndDrop subTracks +visibility hide +group compGeno +noInherit on +priority 240 +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 +matrixHeader A, C, G, T +otherDb canFam4 +chainMinScore 3000 +chainLinearGap medium +spectrum on +html chainNet + + track chainNetCanFam4Viewchain + shortLabel Chain + view chain + visibility pack + parent chainNetCanFam4 + spectrum on + + track chainCanFam4 + parent chainNetCanFam4Viewchain + subGroups view=chain + shortLabel $o_Organism Chain + longLabel $o_Organism ($o_date) Chained Alignments + type chain canFam4 + html chainNet + + track chainNetCanFam4Viewnet + shortLabel Net + view net + visibility full + parent chainNetCanFam4 + + track netCanFam4 + parent chainNetCanFam4Viewnet + subGroups view=net + shortLabel $o_Organism Net + longLabel $o_Organism ($o_date) Alignment Net + type netAlign canFam4 chainCanFam4 + html chainNet + +################################################################ +# canFam3 - dog 'Tasha' - Canis lupus familiaris - mammal - 9615 +################################################################ +track chainNetCanFam3 +compositeTrack on +shortLabel $o_Organism Chain/Net +longLabel $o_Organism ($o_date), Chain and Net Alignments +subGroup1 view Views chain=Chain net=Net +dragAndDrop subTracks +visibility hide +group compGeno +noInherit on +priority 240 +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 +matrixHeader A, C, G, T +otherDb canFam3 +chainMinScore 3000 +chainLinearGap medium +spectrum on +html chainNet + + track chainNetCanFam3Viewchain + shortLabel Chain + view chain + visibility pack + parent chainNetCanFam3 + spectrum on + + track chainCanFam3 + parent chainNetCanFam3Viewchain + subGroups view=chain + shortLabel $o_Organism Chain + longLabel $o_Organism ($o_date) Chained Alignments + type chain canFam3 + html chainNet + + track chainNetCanFam3Viewnet + shortLabel Net + view net + visibility full + parent chainNetCanFam3 + + track netCanFam3 + parent chainNetCanFam3Viewnet + subGroups view=net + shortLabel $o_Organism Net + longLabel $o_Organism ($o_date) Alignment Net + type netAlign canFam3 chainCanFam3 + html chainNet + +################################################################ +# canFam2 - dog 'Tasha' - Canis lupus familiaris - mammal - 9615 +################################################################ +track chainNetCanFam2 +compositeTrack on +shortLabel $o_Organism Chain/Net +longLabel $o_Organism ($o_date), Chain and Net Alignments +subGroup1 view Views chain=Chain net=Net +dragAndDrop subTracks +visibility hide +group compGeno +noInherit on +priority 240 +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 +matrixHeader A, C, G, T +otherDb canFam2 +chainMinScore 3000 +chainLinearGap medium +spectrum on +html chainNet + + track chainNetCanFam2Viewchain + shortLabel Chain + view chain + visibility pack + parent chainNetCanFam2 + spectrum on + + track chainCanFam2 + parent chainNetCanFam2Viewchain + subGroups view=chain + shortLabel $o_Organism Chain + longLabel $o_Organism ($o_date) Chained Alignments + type chain canFam2 + html chainNet + + track chainNetCanFam2Viewnet + shortLabel Net + view net + visibility full + parent chainNetCanFam2 + + track netCanFam2 + parent chainNetCanFam2Viewnet + subGroups view=net + shortLabel $o_Organism Net + longLabel $o_Organism ($o_date) Alignment Net + type netAlign canFam2 chainCanFam2 + html chainNet + +################################################################ +# canFamPoodle1 - dog - Canis lupus familiaris - mammal - 9615 +# Venter's poodle 'Shadow' +################################################################ +track chainNetPoodle +compositeTrack on +shortLabel Poodle Chain/Net +longLabel Poodle Chain and Net Alignments +subGroup1 view Views chain=Chains net=Nets +dragAndDrop subTracks +visibility hide +group compGeno +noInherit on +priority 500 +color 0,0,0 +altColor 100,50,0 +type bed 3 +sortOrder view=+ + + track chainNetPoodleViewchain + shortLabel Chains + view chain + visibility pack + parent chainNetPoodle + spectrum on + + track chainCanFamPoodle1 + parent chainNetPoodleViewchain off + subGroups view=chain + shortLabel $o_Organism Chain + longLabel $o_Organism ($o_date) Chained Alignments + color 0,0,0 + altColor 100,50,0 + matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91 + matrixHeader A, C, G, T + type chain canFamPoodle1 + otherDb canFamPoodle1 + + track chainNetPoodleViewnet + shortLabel Nets + view net + visibility full + parent chainNetPoodle + + track netCanFamPoodle1 + parent chainNetPoodleViewnet off + subGroups view=net + shortLabel $o_Organism Net + longLabel $o_Organism ($o_date) Alignment Net + type netAlign canFamPoodle1 chainCanFamPoodle1 + otherDb canFamPoodle1 +