cad24d48147c54fec5574b6841027b1d51a9fdf3 hiram Thu Jan 7 17:49:28 2021 -0800 adding chainNet plus mafNet alignments for assembly hub chainNet tracks refs #26584 diff --git src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra index cb899f2..e916765 100644 --- src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra +++ src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra @@ -1,168 +1,170 @@ -################################################################ -# GCF_003668045.3_CriGri-PICRH-1.0 - Chinese hamster - Cricetulus griseus - mammals -################################################################ -track chainNetGCF_003668045.3 +############################################################################## +# GCA_901343595v1_MONAX5 - woodchuck - Marmota monax - mammal +############################################################################## +track chainNetGCA_901343595v1 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 200.3 color 0,0,0 altColor 255,255,0 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 GCF_003668045.3 +otherDb GCA_901343595v1 chainMinScore 3000 chainLinearGap medium spectrum on html chainNet - track chainNetGCF_003668045.3Viewchain + track chainNetGCA_901343595v1Viewchain shortLabel Chain view chain visibility pack - parent chainNetGCF_003668045.3 + parent chainNetGCA_901343595v1 spectrum on - track chainGCF_003668045.3_CriGri-PICRH-1.0i - parent chainNetGCF_003668045.3Viewchain + track chainGCA_901343595v1_MONAX5 + parent chainNetGCA_901343595v1Viewchain subGroups view=chain shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments - type bigChain GCF_003668045.3 - bigDataUrl /gbdb/mm39/bbi/chainNet/chainGCF_003668045.3.bb - linkDataUrl /gbdb/mm39/bbi/chainNet/chainGCF_003668045.3Link.bb + type chain GCA_901343595v1 html chainNet - track chainNetGCF_003668045.3Viewnet + track chainNetGCA_901343595v1Viewnet shortLabel Net view net visibility dense - parent chainNetGCF_003668045.3 + parent chainNetGCA_901343595v1 - track netGCF_003668045.3_CriGri-PICRH-1.0i - parent chainNetGCF_003668045.3Viewnet + track netGCA_901343595v1_MONAX5 + parent chainNetGCA_901343595v1Viewnet subGroups view=net shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net - type netAlign GCF_003668045.3 chainGCF_003668045.3_CriGri-PICRH-1.0i + type netAlign GCA_901343595v1 chainGCA_901343595v1_MONAX5 html chainNet -################################################################ -################################################################ -# GCA_901343595v1_MONAX5 - woodchuck - Marmota monax - mammal -################################################################ -track chainNetGCA_901343595v1 +############################################################################## +# GCF_003668045.3 - Chinese hamster - Cricetulus griseus - taxId: 10029 - mammal +############################################################################## +track chainNetGCF_003668045.3 compositeTrack on -shortLabel $o_Organism Chain/Net -longLabel $o_Organism ($o_date), Chain and Net Alignments +shortLabel Chinese hamster Chain/Net +longLabel Chinese hamster (Jun. 2020 GCF_003668045.3_CriGri-PICRH-1.0), Chain and Net Alignments subGroup1 view Views chain=Chain net=Net dragAndDrop subTracks visibility hide group compGeno noInherit on -priority 200.3 +priority 100.1 color 0,0,0 -altColor 255,255,0 +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 GCA_901343595v1 -chainMinScore 3000 chainLinearGap medium -spectrum on +chainMinScore 3000 +matrixHeader A, C, G, T +otherDb GCF_003668045.3 html chainNet - track chainNetGCA_901343595v1Viewchain + track chainNetGCF_003668045.3Viewchain shortLabel Chain view chain visibility pack - parent chainNetGCA_901343595v1 + parent chainNetGCF_003668045.3 spectrum on - track chainGCA_901343595v1_MONAX5 - parent chainNetGCA_901343595v1Viewchain + track chainGCF_003668045.3 + parent chainNetGCF_003668045.3Viewchain subGroups view=chain - shortLabel $o_Organism Chain - longLabel $o_Organism ($o_date) Chained Alignments - type chain GCA_901343595v1 + shortLabel Chinese hamster Chain + longLabel Chinese hamster (Jun. 2020 GCF_003668045.3_CriGri-PICRH-1.0) Chained Alignments + type bigChain GCF_003668045.3 + bigDataUrl /gbdb/mm39/bbi/chainNet/chainGCF_003668045.3.bb + linkDataUrl /gbdb/mm39/bbi/chainNet/chainGCF_003668045.3Link.bb html chainNet - track chainNetGCA_901343595v1Viewnet + track mafNetGCF_003668045.3Viewnet shortLabel Net view net - visibility dense - parent chainNetGCA_901343595v1 + visibility full + parent chainNetGCF_003668045.3 - track netGCA_901343595v1_MONAX5 - parent chainNetGCA_901343595v1Viewnet + track netGCF_003668045.3 + parent mafNetGCF_003668045.3Viewnet subGroups view=net - shortLabel $o_Organism Net - longLabel $o_Organism ($o_date) Alignment Net - type netAlign GCA_901343595v1 chainGCA_901343595v1_MONAX5 + shortLabel Chinese hamster mafNet + longLabel Chinese hamster (Jun. 2020 GCF_003668045.3_CriGri-PICRH-1.0) mafNet Alignment + type bigMaf + bigDataUrl /gbdb/mm39/bbi/chainNet/mm39.GCF_003668045.3.net.bb + summary /gbdb/mm39/bbi/chainNet/mm39.GCF_003668045.3.net.summary.bb + speciesOrder GCF_003668045.3 html chainNet -################################################################ -# GCF_009829145.1_bChiLan1.pri - lance-tailed manakin - Chiroxiphia lanceolata - birds -################################################################ +############################################################################## +# GCF_009829145.1 - lance-tailed manakin - Chiroxiphia lanceolata - taxId: 296741 - birds +############################################################################## track chainNetGCF_009829145.1 compositeTrack on -shortLabel $o_Organism Chain/Net -longLabel $o_Organism ($o_date), Chain and Net Alignments +shortLabel lance-tailed manakin Chain/Net +longLabel lance-tailed manakin (Jan. 2020 GCF_009829145.1_bChiLan1.pri), Chain and Net Alignments subGroup1 view Views chain=Chain net=Net dragAndDrop subTracks visibility hide group compGeno noInherit on -priority 200.3 +priority 100.1 color 0,0,0 -altColor 255,255,0 +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 GCF_009829145.1 chainMinScore 3000 chainLinearGap medium -spectrum on +matrixHeader A, C, G, T +otherDb GCF_009829145.1 html chainNet track chainNetGCF_009829145.1Viewchain shortLabel Chain view chain visibility pack parent chainNetGCF_009829145.1 spectrum on - track chainGCF_009829145.1_bChiLan1.pri + track chainGCF_009829145.1 parent chainNetGCF_009829145.1Viewchain subGroups view=chain - shortLabel $o_Organism Chain - longLabel $o_Organism ($o_date) Chained Alignments + shortLabel lance-tailed manakin Chain + longLabel lance-tailed manakin (Jan. 2020 GCF_009829145.1_bChiLan1.pri) Chained Alignments type bigChain GCF_009829145.1 bigDataUrl /gbdb/mm39/bbi/chainNet/chainGCF_009829145.1.bb linkDataUrl /gbdb/mm39/bbi/chainNet/chainGCF_009829145.1Link.bb html chainNet - track chainNetGCF_009829145.1Viewnet + track mafNetGCF_009829145.1Viewnet shortLabel Net view net - visibility dense + visibility full parent chainNetGCF_009829145.1 - track netGCF_009829145.1_bChiLan1.pri - parent chainNetGCF_009829145.1Viewnet + track netGCF_009829145.1 + parent mafNetGCF_009829145.1Viewnet subGroups view=net - shortLabel $o_Organism Net - longLabel $o_Organism ($o_date) Alignment Net - type netAlign GCF_009829145.1 chainGCF_009829145.1_bChiLan1.pri + shortLabel lance-tailed manakin mafNet + longLabel lance-tailed manakin (Jan. 2020 GCF_009829145.1_bChiLan1.pri) mafNet Alignment + type bigMaf + bigDataUrl /gbdb/mm39/bbi/chainNet/mm39.GCF_009829145.1.net.bb + summary /gbdb/mm39/bbi/chainNet/mm39.GCF_009829145.1.net.summary.bb + speciesOrder GCF_009829145.1 html chainNet -################################################################