# configuration file for GenBank/RefSeq alignment process # # $Id: genbank.conf,v 1.371 2010/05/28 17:59:39 chinhli Exp $ # ## # cluster configuration ## # swarm cluster.rootDir = /hive/data/outside/genbank/build cluster.paraHub = swarm ## # only allow build on designated server ## build.server = hgwdev ## # Root where grepIndex files are build ## grepIndex.rootDir = /data/tmp/grepIndex ## # default values, which can be overridden for each genome ## ## # Alignment genome partition window and overlap sizes. Default values were # chosen to balance number of jobs, average run time and longest jobs for # human mRNA alignments. ## default.align.window = 80000000 default.align.overlap = 3000000 default.align.maxGap = 3000000 default.align.maxJobTargetSize = 80000000 ## # Minimum size of an unplaced seq to process, smaller sequences are skipped. # Value suggested by Jim Kent. "logical place to cut off is 'contigs' that # are composed of single reads, the single read size these days tends to be # about 750. So perhaps a cut off of 900." default.align.minUnplacedSize = 900 ## # max size of query fasta files to create, in megabytes. ## default.align.querySplitSize = 4 ## # pslCDnaFilter parameters variable definitions by genome assembly category, # and type of cDNA sequence. # # The assembly categories are: # - finished - high qualify # - ordered - well ordered, whole genome shotgun # - lowCover - low coverage (< 4x), lots of contigs, N50 scaffold size < 1mb ## # common paramters used for all assembly categories var.common.refseq.mrna.native.pslCDnaFilter = -minQSize=20 -minNonRepSize=16 -ignoreNs -bestOverlap -polyASizes var.common.refseq.mrna.xeno.pslCDnaFilter = -minQSize=20 -minNonRepSize=40 -ignoreNs -bestOverlap -polyASizes var.common.genbank.mrna.native.pslCDnaFilter = -minQSize=20 -minNonRepSize=16 -ignoreNs -bestOverlap -polyASizes var.common.genbank.mrna.xeno.pslCDnaFilter = -minQSize=20 -minNonRepSize=40 -ignoreNs -bestOverlap -polyASizes var.common.genbank.est.native.pslCDnaFilter = -minQSize=20 -minNonRepSize=16 -ignoreNs -bestOverlap -polyASizes -usePolyTHead var.common.genbank.est.xeno.pslCDnaFilter = -minQSize=20 -minNonRepSize=40 -ignoreNs -bestOverlap -polyASizes -usePolyTHead # common paramters used for local near best filtering var.localNB.refseq.mrna.native.pslCDnaFilter = -localNearBest=0.001 ${common.refseq.mrna.native.pslCDnaFilter} var.localNB.refseq.mrna.xeno.pslCDnaFilter = -localNearBest=0.010 ${common.refseq.mrna.xeno.pslCDnaFilter} var.localNB.genbank.mrna.native.pslCDnaFilter = -localNearBest=0.005 ${common.genbank.mrna.native.pslCDnaFilter} var.localNB.genbank.mrna.xeno.pslCDnaFilter = -localNearBest=0.010 ${common.genbank.mrna.xeno.pslCDnaFilter} var.localNB.genbank.est.native.pslCDnaFilter = -localNearBest=0.005 ${common.genbank.est.native.pslCDnaFilter} var.localNB.genbank.est.xeno.pslCDnaFilter = -localNearBest=0.010 ${common.genbank.est.xeno.pslCDnaFilter} # common paramters used for global near best filtering var.globalNB.refseq.mrna.native.pslCDnaFilter = -globalNearBest=0.0010 ${common.refseq.mrna.native.pslCDnaFilter} var.globalNB.refseq.mrna.xeno.pslCDnaFilter = -globalNearBest=0.0100 ${common.refseq.mrna.xeno.pslCDnaFilter} var.globalNB.genbank.mrna.native.pslCDnaFilter = -globalNearBest=0.0025 ${common.genbank.mrna.native.pslCDnaFilter} var.globalNB.genbank.mrna.xeno.pslCDnaFilter = -globalNearBest=0.0100 ${common.genbank.mrna.xeno.pslCDnaFilter} var.globalNB.genbank.est.native.pslCDnaFilter = -globalNearBest=0.0025 ${common.genbank.est.native.pslCDnaFilter} var.globalNB.genbank.est.xeno.pslCDnaFilter = -globalNearBest=0.0100 ${common.genbank.est.xeno.pslCDnaFilter} # finished assemblies var.finished.refseq.mrna.native.pslCDnaFilter = -minId=0.95 -minCover=0.25 ${globalNB.refseq.mrna.native.pslCDnaFilter} var.finished.refseq.mrna.xeno.pslCDnaFilter = -minId=0.35 -minCover=0.25 ${globalNB.refseq.mrna.xeno.pslCDnaFilter} var.finished.genbank.mrna.native.pslCDnaFilter = -minId=0.95 -decayMinCover ${globalNB.genbank.mrna.native.pslCDnaFilter} var.finished.genbank.mrna.xeno.pslCDnaFilter = -minId=0.35 -minCover=0.25 ${globalNB.genbank.mrna.xeno.pslCDnaFilter} var.finished.genbank.est.native.pslCDnaFilter = -minId=0.95 -minCover=0.25 ${globalNB.genbank.est.native.pslCDnaFilter} var.finished.genbank.est.xeno.pslCDnaFilter = -minId=0.10 -minCover=0.10 ${globalNB.genbank.est.xeno.pslCDnaFilter} # well-ordered assemblies var.ordered.refseq.mrna.native.pslCDnaFilter = -minId=0.95 -minCover=0.15 ${localNB.refseq.mrna.native.pslCDnaFilter} var.ordered.refseq.mrna.xeno.pslCDnaFilter = -minId=0.35 -minCover=0.15 ${localNB.refseq.mrna.xeno.pslCDnaFilter} var.ordered.genbank.mrna.native.pslCDnaFilter = -minId=0.95 -minCover=0.15 ${localNB.genbank.mrna.native.pslCDnaFilter} var.ordered.genbank.mrna.xeno.pslCDnaFilter = -minId=0.35 -minCover=0.15 ${localNB.genbank.mrna.xeno.pslCDnaFilter} var.ordered.genbank.est.native.pslCDnaFilter = -minId=0.95 -minCover=0.15 ${localNB.genbank.est.native.pslCDnaFilter} var.ordered.genbank.est.xeno.pslCDnaFilter = -minId=0.35 -minCover=0.10 ${localNB.genbank.est.xeno.pslCDnaFilter} # low-coverage assemblies var.lowCover.refseq.mrna.native.pslCDnaFilter = -minId=0.94 -minAlnSize=80 ${localNB.refseq.mrna.native.pslCDnaFilter} var.lowCover.refseq.mrna.xeno.pslCDnaFilter = -minId=0.33 -minAlnSize=80 ${localNB.refseq.mrna.xeno.pslCDnaFilter} var.lowCover.genbank.mrna.native.pslCDnaFilter = -minId=0.94 -minAlnSize=80 ${localNB.genbank.mrna.native.pslCDnaFilter} var.lowCover.genbank.mrna.xeno.pslCDnaFilter = -minId=0.33 -minAlnSize=80 ${localNB.genbank.mrna.xeno.pslCDnaFilter} var.lowCover.genbank.est.native.pslCDnaFilter = -minId=0.94 -minAlnSize=50 ${localNB.genbank.est.native.pslCDnaFilter} var.lowCover.genbank.est.xeno.pslCDnaFilter = -minId=0.33 -minAlnSize=50 ${localNB.genbank.est.xeno.pslCDnaFilter} default.perChromTables = yes default.genbank.mrna.native.load = yes default.genbank.mrna.native.loadDesc = yes default.genbank.mrna.xeno.load = no default.genbank.mrna.xeno.loadDesc = no default.genbank.est.native.load = yes default.genbank.est.native.loadDesc = no default.genbank.est.xeno.load = no default.genbank.est.xeno.loadDesc = no default.refseq.mrna.native.load = yes default.refseq.mrna.native.loadDesc = yes default.refseq.mrna.xeno.load = yes default.refseq.mrna.xeno.loadDesc = yes ## # genome configurations ## # hg15test - used for debugging hg15test.serverGenome = /hive/data/genomes/hg15/nib/chr*.nib hg15test.clusterGenome = /scratch/data/hg15/chromTrfMixedNib/chr*.nib hg15test.ooc = /scratch/data/hg15/11.ooc hg15test.lift = /hive/data/genomes/hg15/jkStuff/liftAll.lft #hg15test.align.unplacedChroms = chrUn_random hg15test.align.unplacedChroms = chr*_random hg15test.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} hg15test.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} hg15test.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} hg15test.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} hg15test.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} hg15test.mgc = yes hg15test.orfeome = yes hg15test.downloadDir = 10april1970 hg15test.genbank.mrna.blatTargetDb = yes hg15test.refseq.mrna.blatTargetDb = yes # hg16 hg16.serverGenome = /hive/data/genomes/hg16/hg16.2bit hg16.clusterGenome = /scratch/data/hg16/bothMaskedNibs/chr*.nib hg16.ooc = /scratch/data/hg16/11.ooc hg16.lift = /hive/data/genomes/hg16/jkStuff/liftAll.lft hg16.align.unplacedChroms = chrUn_random hg16.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} hg16.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} hg16.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} hg16.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} hg16.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} hg16.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} hg16.genbank.est.xeno.load = yes hg16.genbank.mrna.xeno.load = yes hg16.mgc = yes hg16.upstreamGeneTbl = refGene hg16.upstreamMaf = mzPt1Mm3Rn3Gg2_pHMM /hive/data/genomes/hg16/bed/multiz.hg16mm3rn3panTro1galGal2/species.lst # hg17 hg17.serverGenome = /hive/data/genomes/hg17/hg17.2bit hg17.clusterGenome = /scratch/data/hg17/hg17.2bit hg17.ooc = /scratch/data/hg17/11.ooc hg17.lift = /hive/data/genomes/hg17/jkStuff/liftAll.lft hg17.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} hg17.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} hg17.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} hg17.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} hg17.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} hg17.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} hg17.genbank.mrna.xeno.load = yes hg17.genbank.est.xeno.load = yes hg17.refseq.mrna.xeno.load = yes hg17.refseq.mrna.xeno.loadDesc = yes hg17.mgc = yes hg17.orfeome = yes hg17.downloadDir = hg17 hg17.upstreamGeneTbl = refGene hg17.upstreamMaf = multiz17way /hive/data/genomes/hg17/bed/multiz17way/species.lst # hg18 hg18.serverGenome = /hive/data/genomes/hg18/hg18.2bit hg18.clusterGenome = /scratch/data/hg18/hg18.2bit hg18.ooc = /scratch/data/hg18/11.ooc hg18.lift = /hive/data/genomes/hg18/jkStuff/liftAll.lft hg18.hapRegions = /hive/data/genomes/hg18/bed/haplotypePos/haplotypePos.psl hg18.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} hg18.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} hg18.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} hg18.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} hg18.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} hg18.genbank.est.xeno.pslCDnaFilter = ${finished.genbank.est.xeno.pslCDnaFilter} hg18.genbank.mrna.xeno.load = yes hg18.genbank.est.xeno.load = yes hg18.refseq.mrna.xeno.load = yes hg18.refseq.mrna.xeno.loadDesc = yes hg18.mgc = yes hg18.orfeome = yes hg18.downloadDir = hg18 hg18.ccds.ncbiBuild = 36.3 hg18.upstreamGeneTbl = refGene hg18.upstreamMaf = multiz28way /hive/data/genomes/hg18/bed/multiz28way/species.lst multiz44way /hive/data/genomes/hg18/bed/multiz44way/species.list hg18.genbank.mrna.blatTargetDb = yes # hg19 - GRCh37 - Genome Reference Consortium Human Reference 37 # Assembly Accession: GCA_000001405.1 hg19.serverGenome = /hive/data/genomes/hg19/hg19.2bit hg19.clusterGenome = /scratch/data/hg19/hg19.2bit hg19.ooc = /scratch/data/hg19/11.ooc hg19.lift = /hive/data/genomes/hg19/jkStuff/hg19.unBridged.lift hg19.hapRegions = /hive/data/genomes/hg19/jkStuff/hg19.haplotypes.psl hg19.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} hg19.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} hg19.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} hg19.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} hg19.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} hg19.genbank.est.xeno.pslCDnaFilter = ${finished.genbank.est.xeno.pslCDnaFilter} hg19.genbank.mrna.xeno.load = yes hg19.genbank.est.xeno.load = yes hg19.refseq.mrna.xeno.load = yes hg19.refseq.mrna.xeno.loadDesc = yes hg19.mgc = yes hg19.orfeome = yes hg19.downloadDir = hg19 hg19.ccds.ncbiBuild = 103.0 hg19.upstreamGeneTbl = refGene hg19.upstreamMaf = multiz46way /hive/data/genomes/hg19/bed/multiz46way/species.list hg19.genbank.mrna.blatTargetDb = yes hg19.perChromTables = no # mm7 mm7.serverGenome = /hive/data/genomes/mm7/mm7.2bit mm7.clusterGenome = /scratch/data/mm7/mm7.2bit mm7.ooc = /scratch/data/mm7/11.ooc mm7.align.unplacedChroms = chrUn_random mm7.lift = /hive/data/genomes/mm7/jkStuff/liftAll.lft mm7.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} mm7.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} mm7.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} mm7.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} mm7.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} mm7.downloadDir = mm7 mm7.refseq.mrna.xeno.load = yes mm7.refseq.mrna.xeno.loadDesc = yes mm7.genbank.mrna.xeno.load = yes mm7.mgc = yes mm7.upstreamGeneTbl = refGene # mm8 mm8.serverGenome = /hive/data/genomes/mm8/mm8.2bit mm8.clusterGenome = /scratch/data/mm8/mm8.2bit mm8.ooc = /scratch/data/mm8/11.ooc mm8.align.unplacedChroms = chrUn_random mm8.lift = /hive/data/genomes/mm8/jkStuff/liftAll.lft mm8.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} mm8.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} mm8.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} mm8.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} mm8.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} mm8.downloadDir = mm8 mm8.refseq.mrna.xeno.load = yes mm8.refseq.mrna.xeno.loadDesc = yes mm8.genbank.mrna.xeno.load = yes mm8.mgc = yes mm8.upstreamGeneTbl = refGene mm8.upstreamMaf = multiz17way /hive/data/genomes/mm8/bed/multiz17way/species.lst # mm9 mm9.serverGenome = /hive/data/genomes/mm9/mm9.2bit mm9.clusterGenome = /scratch/data/mm9/mm9.2bit mm9.ooc = /scratch/data/mm9/11.ooc mm9.align.unplacedChroms = *_random mm9.lift = /hive/data/genomes/mm9/jkStuff/nonBridgedGap.lft mm9.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} mm9.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} mm9.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} mm9.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} mm9.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} mm9.downloadDir = mm9 mm9.refseq.mrna.xeno.load = yes mm9.refseq.mrna.xeno.loadDesc = yes mm9.genbank.mrna.xeno.load = yes mm9.mgc = yes mm9.orfeome = yes mm9.ccds.ncbiBuild = 37.2 mm9.upstreamGeneTbl = refGene mm9.upstreamMaf = multiz30way /hive/data/genomes/mm9/bed/multiz30way/species.list mm9.genbank.mrna.blatTargetDb = yes # mm10 mm10.serverGenome = /hive/data/genomes/mm10/mm10.2bit mm10.clusterGenome = /scratch/data/mm10/mm10.2bit mm10.ooc = /scratch/data/mm10/mm10.11.ooc mm10.lift = /scratch/data/mm10/mm10.nonBridged.lift mm10.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} mm10.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} mm10.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} mm10.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} mm10.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} mm10.downloadDir = mm10 mm10.refseq.mrna.xeno.load = yes mm10.refseq.mrna.xeno.loadDesc = yes mm10.genbank.mrna.xeno.load = yes mm10.mgc = yes mm10.orfeome = yes mm10.ccds.ncbiBuild = 38.1 mm10.genbank.mrna.blatTargetDb = yes # mm10.ccds.ncbiBuild = 37.2 # mm10.upstreamGeneTbl = refGene # mm10.upstreamMaf = multiz30way /hive/data/genomes/mm10/bed/multiz30way/species.list # rn3 rn3.serverGenome = /hive/data/genomes/rn3/nib/chr*.nib rn3.clusterGenome = /scratch/data/rn3/softNib/chr*.nib rn3.ooc = /scratch/data/rn3/11.ooc rn3.align.unplacedChroms = chrUn,chrUn_random rn3.lift = /hive/data/genomes/rn3/jkStuff/liftAll.lft rn3.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} rn3.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} rn3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} rn3.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} rn3.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} rn3.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} rn3.genbank.mrna.xeno.load = yes rn3.downloadDir = rnJun2003 rn3.refseq.mrna.xeno.load = yes rn3.mgc = yes rn3.upstreamGeneTbl = refGene # rn4 rn4.serverGenome = /hive/data/genomes/rn4/rn4.2bit rn4.clusterGenome = /scratch/data/rn4/rn4.2bit rn4.ooc = /scratch/data/rn4/11.ooc rn4.align.unplacedChroms = chrUn,chr*_random rn4.lift = /hive/data/genomes/rn4/jkStuff/liftAll.lft rn4.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} rn4.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} rn4.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} rn4.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} rn4.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} rn4.downloadDir = rn4 rn4.refseq.mrna.xeno.load = yes rn4.refseq.mrna.xeno.loadDesc = yes rn4.genbank.mrna.xeno.load = yes rn4.mgc = yes rn4.upstreamGeneTbl = refGene rn4.upstreamMaf = multiz9way /hive/data/genomes/rn4/bed/multiz9way/species.lst # rn5 (rat) rn5.serverGenome = /hive/data/genomes/rn5/rn5.2bit rn5.clusterGenome = /hive/data/genomes/rn5/rn5.2bit rn5.ooc = /hive/data/genomes/rn5/jkStuff/rn5.11.ooc rn5.lift = /hive/data/genomes/rn5/jkStuff/rn5.nonBridged.lift rn5.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} rn5.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} rn5.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} rn5.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} rn5.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} rn5.downloadDir = rn5 rn5.refseq.mrna.xeno.load = yes rn5.refseq.mrna.xeno.loadDesc = yes rn5.genbank.mrna.xeno.load = yes rn5.perChromTables = no rn5.mgc = yes # rn5.upstreamGeneTbl = refGene # rn5.upstreamMaf = multiz9way # /hive/data/genomes/rn5/bed/multiz9way/species.lst # hetGla2 (moleRat) hetGla2.serverGenome = /hive/data/genomes/hetGla2/hetGla2.2bit hetGla2.clusterGenome = /hive/data/genomes/hetGla2/hetGla2.2bit hetGla2.ooc = /hive/data/hetGla2/jkStuff/hetGla2.11.ooc hetGla2.lift = no hetGla2.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} hetGla2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} hetGla2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} hetGla2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} hetGla2.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} hetGla2.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} hetGla2.refseq.mrna.native.load = no hetGla2.refseq.mrna.xeno.load = yes hetGla2.genbank.mrna.native.load = no hetGla2.genbank.mrna.xeno.load = yes hetGla2.genbank.est.native.load = no hetGla2.downloadDir = hetGla2 hetGla2.perChromTables = no # hetGla1 (moleRat) hetGla1.serverGenome = /hive/data/genomes/hetGla1/hetGla1.2bit hetGla1.clusterGenome = /scratch/data/hetGla1/hetGla1.2bit hetGla1.ooc = /scratch/data/hetGla1/hetGla1.11.ooc hetGla1.lift = no hetGla1.perChromTables = no hetGla1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} hetGla1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} hetGla1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} hetGla1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} hetGla1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} hetGla1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} hetGla1.downloadDir = hetGla1 hetGla1.refseq.mrna.native.load = no hetGla1.refseq.mrna.xeno.load = yes hetGla1.refseq.mrna.xeno.loadDesc = yes hetGla1.genbank.mrna.native.load = yes hetGla1.genbank.mrna.native.loadDesc = yes hetGla1.genbank.mrna.xeno.load = yes hetGla1.genbank.mrna.xeno.loadDesc = yes hetGla1.genbank.est.native.load = yes hetGla1.genbank.est.native.loadDesc = yes # sarHar1 (Tasmanian Devil) sarHar1.serverGenome = /hive/data/genomes/sarHar1/sarHar1.2bit sarHar1.clusterGenome = /scratch/data/sarHar1/sarHar1.2bit sarHar1.ooc = /scratch/data/sarHar1/sarHar1.11.ooc sarHar1.lift = no sarHar1.perChromTables = no sarHar1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} sarHar1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} sarHar1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} sarHar1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} sarHar1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} sarHar1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} sarHar1.downloadDir = sarHar1 sarHar1.refSeq.native.load = no sarHar1.refseq.mrna.xeno.load = yes sarHar1.refseq.mrna.xeno.loadDesc = yes sarHar1.genbank.mrna.native.load = yes sarHar1.genbank.mrna.native.loadDesc = yes sarHar1.genbank.mrna.xeno.load = yes sarHar1.genbank.mrna.xeno.loadDesc = yes sarHar1.genbank.est.native.load = no sarHar1.genbank.est.native.loadDesc = no # fr1 fr1.serverGenome = /hive/data/genomes/fr1/fr1.2bit fr1.clusterGenome = /scratch/data/fr1/fr1.2bit fr1.ooc = no fr1.align.unplacedChroms = chrUn fr1.lift = /hive/data/genomes/fr1/Un/chrUn-frag.lft fr1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} fr1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} fr1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} fr1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} fr1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} fr1.genbank.mrna.xeno.loadDesc = yes fr1.refseq.mrna.native.load = no fr1.refseq.mrna.xeno.load = no fr1.upstreamGeneTbl = ensGene # fr2 fr2.serverGenome = /hive/data/genomes/fr2/fr2.2bit fr2.clusterGenome = /scratch/data/fr2/fr2.2bit fr2.ooc = /scratch/data/fr2/11.ooc fr2.align.unplacedChroms = chrUn fr2.lift = /hive/data/genomes/fr2/jkStuff/liftAll.lft fr2.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} fr2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} fr2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} fr2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} fr2.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} fr2.genbank.mrna.xeno.loadDesc = yes fr2.genbank.mrna.xeno.load = yes fr2.refseq.mrna.native.load = no fr2.refseq.mrna.xeno.load = no fr2.upstreamGeneTbl = ensGene fr2.upstreamMaf = multiz5way /hive/data/genomes/fr2/bed/multiz5way/species.lst # fr3 fr3.serverGenome = /hive/data/genomes/fr3/fr3.2bit fr3.clusterGenome = /scratch/data/fr3/fr3.2bit fr3.ooc = /scratch/data/fr3/fr3.11.ooc # fr3.lift = /scratch/data/fr3/fr3.nonBridged.lift fr3.perChromTables = no fr3.lift = no fr3.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} fr3.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} fr3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} fr3.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} fr3.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} fr3.genbank.mrna.xeno.loadDesc = yes fr3.refseq.mrna.xeno.load = no fr3.genbank.mrna.xeno.load = yes # fr3.upstreamGeneTbl = ensGene # fr3.upstreamMaf = multiz5way /hive/data/genomes/fr3/bed/multiz5way/species.lst # dm1 dm1.serverGenome = /hive/data/genomes/dm1/nib/chr*.nib dm1.clusterGenome = /scratch/data/dm1/nib/chr*.nib dm1.ooc = /scratch/data/dm1/11.ooc dm1.lift = /hive/data/genomes/dm1/jkStuff/liftAll.lft dm1.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} dm1.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} dm1.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} dm1.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} dm1.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} dm1.genbank.mrna.xeno.load = yes dm1.downloadDir = dm1 # dm2 (D. melanogaster) dm2.serverGenome = /hive/data/genomes/dm2/nib/chr*.nib dm2.clusterGenome = /scratch/data/dm2/nib/chr*.nib dm2.ooc = /scratch/data/dm1/11.ooc dm2.lift = /hive/data/genomes/dm2/jkStuff/liftAll.lft dm2.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} dm2.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} dm2.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} dm2.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} dm2.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} dm2.genbank.mrna.xeno.load = yes dm2.downloadDir = dm2 dm2.upstreamGeneTbl = refGene dm2.upstreamMaf = multiz15way /hive/data/genomes/dm2/bed/multiz15way/species.lst # dm3 (D. melanogaster) dm3.serverGenome = /hive/data/genomes/dm3/dm3.2bit dm3.clusterGenome = /scratch/data/dm3/dm3.2bit dm3.ooc = /scratch/data/dm3/11.ooc dm3.lift = /hive/data/genomes/dm3/jkStuff/liftAll.lft dm3.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} dm3.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} dm3.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} dm3.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} dm3.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} dm3.genbank.mrna.xeno.load = yes # sacCer3 S. cerevisiae sacCer3.serverGenome = /hive/data/genomes/sacCer3/sacCer3.2bit sacCer3.clusterGenome = /scratch/data/sacCer3/sacCer3.2bit sacCer3.ooc = no sacCer3.maxIntron = 5000 sacCer3.lift = no sacCer3.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} sacCer3.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} sacCer3.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} sacCer3.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} sacCer3.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} #sacCer3.perChromTables = no # doesn't work in the browser sacCer3.genbank.mrna.xeno.load = no sacCer3.refseq.mrna.native.load = no sacCer3.downloadDir = sacCer3 # sacCer2 S. cerevisiae sacCer2.serverGenome = /hive/data/genomes/sacCer2/sacCer2.2bit sacCer2.clusterGenome = /scratch/data/sacCer2/sacCer2.2bit sacCer2.ooc = no sacCer2.maxIntron = 5000 sacCer2.lift = no sacCer2.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} sacCer2.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} sacCer2.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} sacCer2.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} sacCer2.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} #sacCer2.perChromTables = no # doesn't work in the browser sacCer2.genbank.mrna.xeno.load = no sacCer2.refseq.mrna.native.load = no sacCer2.downloadDir = sacCer2 # sacCer1 sacCer1.serverGenome = /hive/data/genomes/sacCer1/nib/chr*.nib sacCer1.clusterGenome = /scratch/data/sacCer1/nib/chr*.nib sacCer1.ooc = no sacCer1.maxIntron = 5000 sacCer1.lift = no sacCer1.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} sacCer1.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} sacCer1.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} sacCer1.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} sacCer1.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} #sacCer1.perChromTables = no # doesn't work in the browser sacCer1.genbank.mrna.xeno.load = no sacCer1.refseq.mrna.native.load = no sacCer1.downloadDir = sacCer1 # panPan1 (bonobo) panPan1.serverGenome = /hive/data/genomes/panPan1/panPan1.2bit panPan1.clusterGenome = /hive/data/genomes/panPan1/panPan1.2bit panPan1.ooc = /hive/data/genomes/panPan1/jkStuff/panPan1.11.ooc panPan1.lift = no panPan1.perChromTables = no panPan1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} panPan1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} panPan1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} panPan1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} panPan1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} panPan1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} panPan1.downloadDir = panPan1 panPan1.refseq.mrna.native.load = no panPan1.refseq.mrna.xeno.load = yes panPan1.genbank.mrna.xeno.load = yes panPan1.genbank.est.native.load = no # panTro4 (chimp) panTro4.serverGenome = /hive/data/genomes/panTro4/panTro4.2bit panTro4.clusterGenome = /hive/data/genomes/panTro4/panTro4.2bit panTro4.ooc = /hive/data/genomes/panTro4/jkStuff/panTro4.11.ooc panTro4.lift = /hive/data/genomes/panTro4/jkStuff/panTro4.nonBridged.lift panTro4.perChromTables = no panTro4.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} panTro4.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} panTro4.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} panTro4.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} panTro4.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} panTro4.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} panTro4.downloadDir = panTro4 panTro4.refseq.mrna.native.load = yes panTro4.refseq.mrna.xeno.load = yes panTro4.genbank.mrna.xeno.load = yes panTro4.genbank.mrna.xeno.loadDesc = yes panTro4.genbank.est.native.load = yes # panTro4.upstreamGeneTbl = ensGene # panTro4.upstreamMaf = multiz12way /hive/data/genomes/panTro4/bed/multiz12way/species.list # chimp panTro3.serverGenome = /hive/data/genomes/panTro3/panTro3.2bit panTro3.clusterGenome = /scratch/data/panTro3/panTro3.2bit panTro3.ooc = /scratch/data/panTro3/panTro3.11.ooc panTro3.align.unplacedChroms = chrUn*,chr*_random panTro3.lift = /scratch/data/panTro3/panTro3.nonBridged.lft panTro3.perChromTables = no panTro3.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} panTro3.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} panTro3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} panTro3.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} panTro3.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} panTro3.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} panTro3.downloadDir = panTro3 panTro3.refseq.mrna.native.load = yes panTro3.refseq.mrna.xeno.load = yes panTro3.genbank.mrna.xeno.load = yes panTro3.genbank.mrna.xeno.loadDesc = yes panTro3.genbank.est.native.load = yes panTro3.upstreamGeneTbl = ensGene panTro3.upstreamMaf = multiz12way /hive/data/genomes/panTro3/bed/multiz12way/species.list panTro1.serverGenome = /hive/data/genomes/panTro1/panTro1.2bit panTro1.clusterGenome = /scratch/data/panTro1/panTro1.2bit panTro1.ooc = /scratch/data/panTro1/11.ooc panTro1.align.unplacedChroms = chrUn_random panTro1.lift = /hive/data/genomes/panTro1/jkStuff/liftAll.lft panTro1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} panTro1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} panTro1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} panTro1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} panTro1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} panTro1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} panTro1.downloadDir = panTro1 panTro1.refseq.mrna.native.load = yes panTro1.refseq.mrna.xeno.load = yes panTro1.genbank.mrna.xeno.load = yes panTro1.genbank.mrna.xeno.loadDesc = yes panTro1.genbank.est.native.load = yes panTro1.upstreamGeneTbl = ensGene panTro2.serverGenome = /hive/data/genomes/panTro2/panTro2.2bit panTro2.clusterGenome = /scratch/data/panTro2/panTro2.2bit panTro2.ooc = /scratch/data/panTro2/11.ooc panTro2.align.unplacedChroms = chrUn,chr*_random panTro2.lift = /hive/data/genomes/panTro2/lifts/genbank.lft panTro2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} panTro2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} panTro2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} panTro2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} panTro2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} panTro2.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} panTro2.downloadDir = panTro2 panTro2.refseq.mrna.native.load = yes panTro2.refseq.mrna.xeno.load = yes panTro2.genbank.mrna.xeno.load = yes panTro2.genbank.mrna.xeno.loadDesc = yes panTro2.genbank.est.native.load = yes panTro2.upstreamGeneTbl = refGene # Gorilla gorGor3.serverGenome = /hive/data/genomes/gorGor3/gorGor3.2bit gorGor3.clusterGenome = /scratch/data/gorGor3/gorGor3.2bit gorGor3.ooc = /scratch/data/gorGor3/gorGor3.11.ooc gorGor3.lift = no gorGor3.perChromTables = no gorGor3.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} gorGor3.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} gorGor3.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} gorGor3.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} gorGor3.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} gorGor3.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} gorGor3.downloadDir = gorGor3 gorGor3.refseq.mrna.native.load = no gorGor3.refseq.mrna.xeno.load = yes gorGor3.refseq.mrna.xeno.loadDesc = yes gorGor3.genbank.mrna.xeno.load = yes gorGor3.genbank.est.native.load = no gorGor3.upstreamGeneTbl = ensGene gorGor3.upstreamMaf = multiz11way /hive/data/genomes/gorGor3/bed/multiz11way/species.list # Baboon # papAnu2 (baboon) papAnu2.serverGenome = /hive/data/genomes/papAnu2/papAnu2.2bit papAnu2.clusterGenome = /hive/data/genomes/papAnu2/papAnu2.2bit papAnu2.ooc = /hive/data/genomes/papAnu2/jkStuff/papAnu2.11.ooc papAnu2.lift = /hive/data/genomes/papAnu2/jkStuff/papAnu2.nonBridged.lift papAnu2.perChromTables = no papAnu2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} papAnu2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} papAnu2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} papAnu2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} papAnu2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} papAnu2.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} papAnu2.downloadDir = papAnu2 papAnu2.refseq.mrna.native.load = yes papAnu2.refseq.mrna.xeno.load = yes papAnu2.genbank.mrna.xeno.load = yes papAnu2.genbank.mrna.xeno.loadDesc = yes papAnu2.genbank.est.native.load = yes papHam1.serverGenome = /hive/data/genomes/papHam1/papHam1.2bit papHam1.clusterGenome = /scratch/data/papHam1/papHam1.2bit papHam1.ooc = /scratch/data/papHam1/papHam1.11.ooc papHam1.lift = no papHam1.perChromTables = no papHam1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} papHam1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} papHam1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} papHam1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} papHam1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} papHam1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} papHam1.downloadDir = papHam1 papHam1.refseq.mrna.native.load = yes papHam1.refseq.mrna.xeno.load = yes papHam1.refseq.mrna.xeno.loadDesc = yes papHam1.genbank.mrna.xeno.load = yes papHam1.genbank.est.native.load = no papHam1.upstreamGeneTbl = xenoRefGene # Orangutan ponAbe2.serverGenome = /hive/data/genomes/ponAbe2/ponAbe2.2bit ponAbe2.clusterGenome = /scratch/data/ponAbe2/ponAbe2.2bit ponAbe2.ooc = /scratch/data/ponAbe2/11.ooc ponAbe2.align.unplacedChroms = chrUn,chr*_random ponAbe2.lift = /hive/data/genomes/ponAbe2/jkStuff/genbank.lft ponAbe2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} ponAbe2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} ponAbe2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} ponAbe2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} ponAbe2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} ponAbe2.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} ponAbe2.downloadDir = ponAbe2 ponAbe2.refseq.mrna.native.load = yes ponAbe2.refseq.mrna.xeno.load = yes ponAbe2.refseq.mrna.xeno.loadDesc = yes ponAbe2.genbank.mrna.xeno.load = yes ponAbe2.upstreamGeneTbl = xenoRefGene ponAbe2.upstreamMaf = multiz8way /hive/data/genomes/ponAbe2/bed/multiz8way/species.list # nomLeu3 (Gibbon) nomLeu3.serverGenome = /hive/data/genomes/nomLeu3/nomLeu3.2bit nomLeu3.clusterGenome = /hive/data/genomes/nomLeu3/nomLeu3.2bit nomLeu3.ooc = /hive/data/genomes/nomLeu3/nomLeu3.11.ooc nomLeu3.lift = /hive/data/genomes/nomLeu3/jkStuff/nomLeu3.nonBridged.lift nomLeu3.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} nomLeu3.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} nomLeu3.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} nomLeu3.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} nomLeu3.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} nomLeu3.genbank.est.xeno.pslCDnaFilter = ${finished.genbank.est.xeno.pslCDnaFilter} nomLeu3.refseq.mrna.native.load = no nomLeu3.refseq.mrna.xeno.load = yes nomLeu3.genbank.mrna.native.load = no nomLeu3.genbank.mrna.xeno.load = yes nomLeu3.genbank.est.native.load = no nomLeu3.downloadDir = nomLeu3 nomLeu3.perChromTables = no # nomLeu2 (Gibbon) nomLeu2.serverGenome = /hive/data/genomes/nomLeu2/nomLeu2.2bit nomLeu2.clusterGenome = /hive/data/genomes/nomLeu2/nomLeu2.2bit nomLeu2.ooc = /hive/data/genomes/nomLeu2/nomLeu2.11.ooc nomLeu2.lift = no nomLeu2.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} nomLeu2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} nomLeu2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} nomLeu2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} nomLeu2.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} nomLeu2.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} nomLeu2.refseq.mrna.native.load = no nomLeu2.refseq.mrna.xeno.load = yes nomLeu2.genbank.mrna.native.load = no nomLeu2.genbank.mrna.xeno.load = yes nomLeu2.genbank.est.native.load = no nomLeu2.downloadDir = nomLeu2 nomLeu2.perChromTables = no # nomLeu1 (Gibbon) nomLeu1.serverGenome = /hive/data/genomes/nomLeu1/nomLeu1.2bit nomLeu1.clusterGenome = /scratch/data/nomLeu1/nomLeu1.2bit nomLeu1.ooc = /scratch/data/nomLeu1/nomLeu1.11.ooc nomLeu1.lift = no nomLeu1.perChromTables = no nomLeu1.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} nomLeu1.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} nomLeu1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} nomLeu1.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} nomLeu1.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} nomLeu1.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} nomLeu1.downloadDir = nomLeu1 nomLeu1.refseq.mrna.native.load = no nomLeu1.refseq.mrna.xeno.load = yes nomLeu1.refseq.mrna.xeno.loadDesc = yes nomLeu1.genbank.mrna.native.load = yes nomLeu1.genbank.mrna.native.loadDesc = yes nomLeu1.genbank.mrna.xeno.load = yes nomLeu1.genbank.mrna.xeno.loadDesc = yes nomLeu1.genbank.est.native.load = no nomLeu1.genbank.est.native.loadDesc = no # Rhesus macaque (macaca mulatta) rheMac2.serverGenome = /hive/data/genomes/rheMac2/rheMac2.2bit rheMac2.clusterGenome = /scratch/data/rheMac2/rheMac2.2bit rheMac2.ooc = /scratch/data/rheMac2/11.ooc rheMac2.lift = no rheMac2.downloadDir = rheMac2 rheMac2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} rheMac2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} rheMac2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} rheMac2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} rheMac2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} rheMac2.genbank.mrna.xeno.load = yes rheMac2.refseq.mrna.native.load = yes rheMac2.refseq.mrna.xeno.load = yes rheMac2.perChromTables = no rheMac2.upstreamGeneTbl = refGene # rheMac3 Rhesus macaque (macaca mulatta) rheMac3.serverGenome = /hive/data/genomes/rheMac3/rheMac3.2bit rheMac3.clusterGenome = /scratch/data/rheMac3/rheMac3.2bit rheMac3.ooc = /scratch/data/rheMac3/rheMac3.11.ooc rheMac3.lift = no rheMac3.perChromTables = no rheMac3.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} rheMac3.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} rheMac3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} rheMac3.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} rheMac3.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} rheMac3.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} rheMac3.downloadDir = rheMac3 rheMac3.genbank.mrna.xeno.load = yes rheMac3.refseq.mrna.native.load = yes rheMac3.refseq.mrna.xeno.load = yes rheMac3.upstreamGeneTbl = refGene # turTru2 (Dolphin) turTru2.serverGenome = /hive/data/genomes/turTru2/turTru2.2bit turTru2.clusterGenome = /hive/data/genomes/turTru2/turTru2.2bit turTru2.ooc = /hive/data/genomes/turTru2/turTru2.11.ooc turTru2.lift = no turTru2.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} turTru2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} turTru2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} turTru2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} turTru2.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} turTru2.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} turTru2.refseq.mrna.native.load = no turTru2.refseq.mrna.xeno.load = yes turTru2.genbank.mrna.native.load = no turTru2.genbank.mrna.xeno.load = no turTru2.genbank.est.native.load = no turTru2.downloadDir = turTru2 turTru2.perChromTables = no # galGal2 (chicken) galGal2.serverGenome = /hive/data/genomes/galGal2/galGal2.2bit galGal2.clusterGenome = /scratch/data/galGal2/nib/chr*.nib galGal2.ooc = /scratch/data/galGal2/11.ooc galGal2.lift = /hive/data/genomes/galGal2/jkStuff/liftAll.lft galGal2.align.unplacedChroms = chrUn galGal2.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} galGal2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} galGal2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} galGal2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} galGal2.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} galGal2.refseq.mrna.native.load = yes galGal2.refseq.mrna.xeno.load = yes galGal2.genbank.mrna.xeno.load = yes galGal2.downloadDir = galGal2 galGal2.upstreamGeneTbl = ensGene # galGal3 galGal3.serverGenome = /hive/data/genomes/galGal3/galGal3.2bit galGal3.clusterGenome = /scratch/data/galGal3/galGal3.2bit galGal3.ooc = /scratch/data/galGal3/11.ooc galGal3.align.unplacedChroms = chr*_random galGal3.lift = /hive/data/genomes/galGal3/jkStuff/liftAll.lft galGal3.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} galGal3.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} galGal3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} galGal3.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} galGal3.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} galGal3.refseq.mrna.native.load = yes galGal3.refseq.mrna.xeno.load = yes galGal3.genbank.mrna.xeno.load = yes galGal3.downloadDir = galGal3 galGal3.upstreamGeneTbl = refGene galGal3.upstreamMaf = multiz7way /hive/data/genomes/galGal3/bed/multiz7way/species.lst # galGal4 (chicken) galGal4.serverGenome = /hive/data/genomes/galGal4/galGal4.2bit galGal4.clusterGenome = /hive/data/genomes/galGal4/galGal4.2bit galGal4.ooc = /hive/data/genomes/galGal4/jkStuff/galGal4.11.ooc galGal4.lift = /hive/data/genomes/galGal4/jkStuff/galGal4.nonBridged.lift galGal4.perChromTables = no galGal4.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} galGal4.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} galGal4.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} galGal4.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} galGal4.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} galGal4.refseq.mrna.native.load = yes galGal4.refseq.mrna.xeno.load = yes galGal4.genbank.mrna.xeno.load = yes galGal4.downloadDir = galGal4 # galGal4.upstreamGeneTbl = refGene # galGal4.upstreamMaf = multiz7way /hive/data/genomes/galGal3/bed/multiz7way/species.lst # melGal1 (turkey) melGal1.serverGenome = /hive/data/genomes/melGal1/melGal1.2bit melGal1.clusterGenome = /scratch/data/melGal1/melGal1.2bit melGal1.ooc = /scratch/data/melGal1/melGal1.11.ooc melGal1.lift = no melGal1.perChromTables = no melGal1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} melGal1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} melGal1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} melGal1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} melGal1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} melGal1.downloadDir = melGal1 melGal1.refseq.mrna.native.load = no melGal1.refseq.mrna.xeno.load = yes melGal1.refseq.mrna.xeno.loadDesc = yes melGal1.genbank.mrna.native.load = yes melGal1.genbank.mrna.native.loadDesc = yes melGal1.genbank.mrna.xeno.load = yes melGal1.genbank.mrna.xeno.loadDesc = yes melGal1.genbank.est.native.load = yes melGal1.genbank.est.native.loadDesc = yes melGal1.upstreamGeneTbl = ensGene # myoLuc2 (Microbat) myoLuc2.serverGenome = /hive/data/genomes/myoLuc2/myoLuc2.2bit myoLuc2.clusterGenome = /scratch/data/myoLuc2/myoLuc2.2bit myoLuc2.ooc = /scratch/data/myoLuc2/myoLuc2.11.ooc myoLuc2.lift = no myoLuc2.perChromTables = no myoLuc2.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} myoLuc2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} myoLuc2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} myoLuc2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} myoLuc2.downloadDir = myoLuc2 myoLuc2.refseq.mrna.native.load = no myoLuc2.refseq.mrna.xeno.load = yes myoLuc2.refseq.mrna.xeno.loadDesc = yes myoLuc2.genbank.mrna.native.load = yes myoLuc2.genbank.mrna.native.loadDesc = yes myoLuc2.genbank.mrna.xeno.load = yes myoLuc2.genbank.mrna.xeno.loadDesc = yes myoLuc2.genbank.est.native.load = no myoLuc2.genbank.est.native.loadDesc = no myoLuc2.upstreamGeneTbl = ensGene # allMiss0 allMis0.serverGenome = /hive/data/genomes/allMis0/allMis0.2bit allMis0.clusterGenome = /scratch/data/allMis0/allMis0.2bit allMis0.ooc = /scratch/data/allMis0/allMis0.11.ooc allMis0.lift = no allMis0.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} allMis0.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} allMis0.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} allMis0.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} allMis0.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} allMis0.refseq.mrna.native.load = yes allMis0.refseq.mrna.xeno.load = yes allMis0.genbank.mrna.xeno.load = yes allMis0.downloadDir = allMis0 allMis0.upstreamGeneTbl = refGene allMis0.perChromTables = no # taeGut1 taeGut1.serverGenome = /hive/data/genomes/taeGut1/taeGut1.2bit taeGut1.clusterGenome = /scratch/data/taeGut1/taeGut1.2bit taeGut1.ooc = /scratch/data/taeGut1/taeGut1.11.ooc taeGut1.align.unplacedChroms = chrUn,chr*_random taeGut1.lift = /hive/data/genomes/taeGut1/jkStuff/liftAll.lft taeGut1.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} taeGut1.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} taeGut1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} taeGut1.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} taeGut1.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} taeGut1.refseq.mrna.native.load = yes taeGut1.refseq.mrna.xeno.load = yes taeGut1.genbank.mrna.xeno.load = yes taeGut1.downloadDir = taeGut1 taeGut1.upstreamGeneTbl = refGene # ce10 (C. elegans) ce10.serverGenome = /hive/data/genomes/ce10/ce10.2bit ce10.clusterGenome = /scratch/data/ce10/ce10.2bit ce10.ooc = /scratch/data/ce10/ce10.11.ooc ce10.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} ce10.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} ce10.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} ce10.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} ce10.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} ce10.maxIntron = 100000 ce10.lift = no ce10.genbank.mrna.xeno.load = yes ce10.refseq.mrna.xeno.load = yes ce10.downloadDir = ce10 ce10.upstreamGeneTbl = ensGene ce10.upstreamMaf = multiz7way /hive/data/genomes/ce10/bed/multiz7way/species.list # ce6 (C. elegans) ce6.serverGenome = /hive/data/genomes/ce6/ce6.2bit ce6.clusterGenome = /scratch/data/ce6/ce6.2bit ce6.ooc = /scratch/data/ce6/11.ooc ce6.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} ce6.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} ce6.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} ce6.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} ce6.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} ce6.maxIntron = 100000 ce6.lift = no ce6.genbank.mrna.xeno.load = yes ce6.refseq.mrna.xeno.load = yes ce6.downloadDir = ce6 ce6.upstreamGeneTbl = ensGene ce6.upstreamMaf = multiz6way /hive/data/genomes/ce6/bed/multiz6way/species.lst # ce4 (C. elegans) ce4.serverGenome = /hive/data/genomes/ce4/ce4.2bit ce4.clusterGenome = /scratch/data/ce4/ce4.2bit ce4.ooc = /scratch/data/ce4/11.ooc ce4.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} ce4.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} ce4.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} ce4.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} ce4.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} ce4.maxIntron = 100000 ce4.lift = no ce4.genbank.mrna.xeno.load = yes ce4.refseq.mrna.xeno.load = yes ce4.downloadDir = ce4 # ce2 (C. elegans) ce2.serverGenome = /hive/data/genomes/ce2/nib/chr*.nib ce2.clusterGenome = /scratch/data/ce2/nib/chr*.nib ce2.ooc = /scratch/data/ce2/11.ooc ce2.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} ce2.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} ce2.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} ce2.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} ce2.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} ce2.maxIntron = 100000 ce2.lift = no ce2.genbank.mrna.xeno.load = no ce2.downloadDir = ce2 ce2.upstreamGeneTbl = refGene # choHof1 (sloth) choHof1.serverGenome = /hive/data/genomes/choHof1/choHof1.2bit choHof1.clusterGenome = /scratch/data/choHof1/choHof1.2bit choHof1.ooc = /scratch/data/choHof1//choHof1.11.ooc choHof1.lift = no choHof1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} choHof1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} choHof1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} choHof1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} choHof1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} choHof1.refseq.mrna.native.load = no choHof1.refseq.mrna.xeno.load = yes choHof1.genbank.mrna.xeno.load = yes choHof1.genbank.est.native.load = no choHof1.downloadDir = choHof1 choHof1.perChromTables = no # chrPic1 (green painted turtle) chrPic1.serverGenome = /hive/data/genomes/chrPic1/chrPic1.2bit chrPic1.clusterGenome = /hive/data/genomes/chrPic1/chrPic1.2bit chrPic1.ooc = /hive/data/genomes/chrPic1/jkStuff/chrPic1.11.ooc chrPic1.lift = no chrPic1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} chrPic1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} chrPic1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} chrPic1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} chrPic1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} chrPic1.refseq.mrna.native.load = no chrPic1.refseq.mrna.xeno.load = yes chrPic1.genbank.mrna.xeno.load = yes chrPic1.genbank.est.native.load = no chrPic1.downloadDir = chrPic1 chrPic1.perChromTables = no # dasNov3 (armadillo) dasNov3.serverGenome = /hive/data/genomes/dasNov3/dasNov3.2bit dasNov3.clusterGenome = /hive/data/genomes/dasNov3/dasNov3.2bit dasNov3.ooc = /hive/data/genomes/dasNov3/jkStuff/dasNov3.11.ooc dasNov3.lift = no dasNov3.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} dasNov3.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} dasNov3.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} dasNov3.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} dasNov3.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} dasNov3.refseq.mrna.native.load = no dasNov3.refseq.mrna.xeno.load = yes dasNov3.genbank.mrna.xeno.load = yes dasNov3.genbank.est.native.load = no dasNov3.downloadDir = dasNov3 dasNov3.perChromTables = no # dipOrd1 (Kangaroo rat) dipOrd1.serverGenome = /hive/data/genomes/dipOrd1/dipOrd1.2bit dipOrd1.clusterGenome = /scratch/data/dipOrd1/dipOrd1.2bit dipOrd1.ooc = /scratch/data/dipOrd1/dipOrd1.11.ooc dipOrd1.lift = no dipOrd1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} dipOrd1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} dipOrd1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} dipOrd1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} dipOrd1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} dipOrd1.refseq.mrna.native.load = no dipOrd1.refseq.mrna.xeno.load = yes dipOrd1.genbank.mrna.xeno.load = yes dipOrd1.genbank.est.native.load = no dipOrd1.downloadDir = dipOrd1 dipOrd1.perChromTables = no # eriEur1 (European Hedgehog) eriEur1.serverGenome = /hive/data/genomes/eriEur1/eriEur1.2bit eriEur1.clusterGenome = /scratch/data/eriEur1/eriEur1.2bit eriEur1.ooc = /scratch/data/eriEur1/eriEur1.11.ooc eriEur1.lift = no eriEur1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} eriEur1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} eriEur1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} eriEur1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} eriEur1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} eriEur1.refseq.mrna.native.load = no eriEur1.refseq.mrna.xeno.load = yes eriEur1.genbank.mrna.xeno.load = no eriEur1.genbank.est.native.load = no eriEur1.downloadDir = eriEur1 eriEur1.perChromTables = no # gadMor1 (Atlantic cod) gadMor1.serverGenome = /hive/data/genomes/gadMor1/gadMor1.2bit gadMor1.clusterGenome = /hive/data/genomes/gadMor1/gadMor1.2bit gadMor1.ooc = /hive/data/genomes/gadMor1/jkStuff/gadMor1.11.ooc gadMor1.lift = no gadMor1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} gadMor1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} gadMor1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} gadMor1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} gadMor1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} gadMor1.refseq.mrna.native.load = no gadMor1.refseq.mrna.xeno.load = yes gadMor1.genbank.mrna.xeno.load = no gadMor1.genbank.est.native.load = yes gadMor1.downloadDir = gadMor1 gadMor1.perChromTables = no # geoFor1 (Medium Ground Finch - Darwin finch) geoFor1.serverGenome = /hive/data/genomes/geoFor1/geoFor1.2bit geoFor1.clusterGenome = /hive/data/genomes/geoFor1/geoFor1.2bit geoFor1.ooc = /hive/data/genomes/geoFor1/jkStuff/geoFor1.11.ooc geoFor1.lift = no geoFor1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} geoFor1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} geoFor1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} geoFor1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} geoFor1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} geoFor1.refseq.mrna.native.load = no geoFor1.refseq.mrna.xeno.load = yes geoFor1.genbank.mrna.xeno.load = no geoFor1.genbank.est.native.load = no geoFor1.downloadDir = geoFor1 geoFor1.perChromTables = no geoFor1.upstreamGeneTbl = xenoRefGene geoFor1.upstreamMaf = multiz7way /hive/data/genomes/geoFor1/bed/multiz7way/species.list # latCha1 (Coelacanth) latCha1.serverGenome = /hive/data/genomes/latCha1/latCha1.2bit latCha1.clusterGenome = /hive/data/genomes/latCha1/latCha1.2bit latCha1.ooc = /hive/data/genomes/latCha1/jkStuff/latCha1.11.ooc latCha1.lift = no latCha1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} latCha1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} latCha1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} latCha1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} latCha1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} latCha1.refseq.mrna.native.load = no latCha1.refseq.mrna.xeno.load = yes latCha1.genbank.mrna.xeno.load = yes latCha1.genbank.est.native.load = no latCha1.downloadDir = latCha1 latCha1.perChromTables = no # melUnd1 (Budgerigar) melUnd1.serverGenome = /hive/data/genomes/melUnd1/melUnd1.2bit melUnd1.clusterGenome = /hive/data/genomes/melUnd1/melUnd1.2bit melUnd1.ooc = /hive/data/genomes/melUnd1/jkStuff/melUnd1.11.ooc melUnd1.lift = no melUnd1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} melUnd1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} melUnd1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} melUnd1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} melUnd1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} melUnd1.refseq.mrna.native.load = no melUnd1.refseq.mrna.xeno.load = yes melUnd1.genbank.mrna.xeno.load = no melUnd1.genbank.est.native.load = no melUnd1.downloadDir = melUnd1 melUnd1.perChromTables = no # micMur1 (Mouse lemur) micMur1.serverGenome = /hive/data/genomes/micMur1/micMur1.2bit micMur1.clusterGenome = /hive/data/genomes/micMur1/micMur1.2bit micMur1.ooc = /hive/data/genomes/micMur1/jkStuff/micMur1.11.ooc micMur1.lift = no micMur1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} micMur1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} micMur1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} micMur1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} micMur1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} micMur1.refseq.mrna.native.load = no micMur1.refseq.mrna.xeno.load = yes micMur1.genbank.mrna.xeno.load = no micMur1.genbank.est.native.load = no micMur1.downloadDir = micMur1 micMur1.perChromTables = no # ochPri2 (Pika) ochPri2.serverGenome = /hive/data/genomes/ochPri2/ochPri2.2bit ochPri2.clusterGenome = /hive/data/genomes/ochPri2/ochPri2.2bit ochPri2.ooc = /hive/data/genomes/ochPri2/jkStuff/ochPri2.11.ooc ochPri2.lift = no ochPri2.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} ochPri2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} ochPri2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} ochPri2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} ochPri2.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} ochPri2.refseq.mrna.native.load = no ochPri2.refseq.mrna.xeno.load = yes ochPri2.genbank.mrna.xeno.load = no ochPri2.genbank.est.native.load = no ochPri2.downloadDir = ochPri2 ochPri2.perChromTables = no # oreNil2 (Nile tilapia) oreNil2.serverGenome = /hive/data/genomes/oreNil2/oreNil2.2bit oreNil2.clusterGenome = /hive/data/genomes/oreNil2/oreNil2.2bit oreNil2.ooc = /hive/data/genomes/oreNil2/jkStuff/oreNil2.11.ooc oreNil2.lift = /hive/data/genomes/oreNil2/jkStuff/oreNil2.nonBridged.lift oreNil2.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} oreNil2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} oreNil2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} oreNil2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} oreNil2.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} oreNil2.refseq.mrna.native.load = yes oreNil2.refseq.mrna.xeno.load = yes oreNil2.genbank.mrna.xeno.load = no oreNil2.genbank.est.native.load = yes oreNil2.downloadDir = oreNil2 oreNil2.perChromTables = no # priPac1 (P. pacificus) priPac1.serverGenome = /hive/data/genomes/priPac1/priPac1.2bit priPac1.clusterGenome = /scratch/data/priPac1/priPac1.2bit priPac1.ooc = /scratch/data/priPac1/11.ooc priPac1.lift = /hive/data/genomes/priPac1/jkStuff/priPac1.supercontigs.lift priPac1.align.unplacedChroms = chrUn priPac1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} priPac1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} priPac1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} priPac1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} priPac1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} priPac1.refseq.mrna.native.load = no priPac1.refseq.mrna.xeno.load = yes priPac1.refseq.mrna.xeno.loadDesc = yes priPac1.genbank.mrna.xeno.load = yes priPac1.genbank.est.native.load = yes priPac1.genbank.est.native.loadDesc = no priPac1.downloadDir = priPac1 priPac1.perChromTables = no # proCap1 (Rock hyrax) proCap1.serverGenome = /hive/data/genomes/proCap1/proCap1.2bit proCap1.clusterGenome = /hive/data/genomes/proCap1/proCap1.2bit proCap1.ooc = /hive/data/genomes/proCap1/jkStuff/proCap1.11.ooc proCap1.lift = no proCap1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} proCap1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} proCap1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} proCap1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} proCap1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} proCap1.refseq.mrna.native.load = no proCap1.refseq.mrna.xeno.load = yes proCap1.genbank.mrna.xeno.load = no proCap1.genbank.est.native.load = no proCap1.downloadDir = proCap1 proCap1.perChromTables = no # pteVam1 (megabat) pteVam1.serverGenome = /hive/data/genomes/pteVam1/pteVam1.2bit pteVam1.clusterGenome = /hive/data/genomes/pteVam1/pteVam1.2bit pteVam1.ooc = /hive/data/genomes/pteVam1/jkStuff/pteVam1.11.ooc pteVam1.lift = no pteVam1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} pteVam1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} pteVam1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} pteVam1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} pteVam1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} pteVam1.refseq.mrna.native.load = no pteVam1.refseq.mrna.xeno.load = yes pteVam1.genbank.mrna.xeno.load = no pteVam1.genbank.est.native.load = no pteVam1.downloadDir = pteVam1 pteVam1.perChromTables = no # saiBol1 (squirrel monkey) saiBol1.serverGenome = /hive/data/genomes/saiBol1/saiBol1.2bit saiBol1.clusterGenome = /hive/data/genomes/saiBol1/saiBol1.2bit saiBol1.ooc = /hive/data/genomes/saiBol1/jkStuff/saiBol1.11.ooc saiBol1.lift = no saiBol1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} saiBol1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} saiBol1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} saiBol1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} saiBol1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} saiBol1.refseq.mrna.native.load = no saiBol1.refseq.mrna.xeno.load = yes saiBol1.genbank.mrna.xeno.load = yes saiBol1.genbank.est.native.load = no saiBol1.downloadDir = saiBol1 saiBol1.perChromTables = no # sorAra1 (common shrew) sorAra1.serverGenome = /hive/data/genomes/sorAra1/sorAra1.2bit sorAra1.clusterGenome = /hive/data/genomes/sorAra1/sorAra1.2bit sorAra1.ooc = /hive/data/genomes/sorAra1/jkStuff/sorAra1.11.ooc sorAra1.lift = no sorAra1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} sorAra1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} sorAra1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} sorAra1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} sorAra1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} sorAra1.refseq.mrna.native.load = no sorAra1.refseq.mrna.xeno.load = yes sorAra1.genbank.mrna.xeno.load = no sorAra1.genbank.est.native.load = no sorAra1.downloadDir = sorAra1 sorAra1.perChromTables = no # speTri2 (13-lined ground squirrel) speTri2.serverGenome = /hive/data/genomes/speTri2/speTri2.2bit speTri2.clusterGenome = /hive/data/genomes/speTri2/speTri2.2bit speTri2.ooc = /hive/data/genomes/speTri2/jkStuff/speTri2.11.ooc speTri2.lift = no speTri2.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} speTri2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} speTri2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} speTri2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} speTri2.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} speTri2.refseq.mrna.native.load = no speTri2.refseq.mrna.xeno.load = yes speTri2.genbank.mrna.xeno.load = no speTri2.genbank.est.native.load = yes speTri2.downloadDir = speTri2 speTri2.perChromTables = no # tarSyr1 (Tarsier) tarSyr1.serverGenome = /hive/data/genomes/tarSyr1/tarSyr1.2bit tarSyr1.clusterGenome = /scratch/data/tarSyr1/tarSyr1.2bit tarSyr1.ooc = /scratch/data/tarSyr1/tarSyr1.11.ooc tarSyr1.lift = no tarSyr1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} tarSyr1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} tarSyr1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} tarSyr1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} tarSyr1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} tarSyr1.refseq.mrna.native.load = no tarSyr1.refseq.mrna.xeno.load = yes tarSyr1.genbank.mrna.xeno.load = no tarSyr1.genbank.est.native.load = yes tarSyr1.downloadDir = tarSyr1 tarSyr1.perChromTables = no # tupBel1 (common shrew) tupBel1.serverGenome = /hive/data/genomes/tupBel1/tupBel1.2bit tupBel1.clusterGenome = /scratch/data/tupBel1/tupBel1.2bit tupBel1.ooc = /scratch/data/tupBel1/tupBel1.11.ooc tupBel1.lift = /hive/data/genomes/tupBel1/jkStuff/tupBel1.nonBridged.lift tupBel1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} tupBel1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} tupBel1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} tupBel1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} tupBel1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} tupBel1.refseq.mrna.native.load = no tupBel1.refseq.mrna.xeno.load = yes tupBel1.genbank.mrna.xeno.load = no tupBel1.genbank.est.native.load = yes tupBel1.downloadDir = tupBel1 tupBel1.perChromTables = no # vicPac1 (alpaca) vicPac1.serverGenome = /hive/data/genomes/vicPac1/vicPac1.2bit vicPac1.clusterGenome = /hive/data/genomes/vicPac1/vicPac1.2bit vicPac1.ooc = /hive/data/genomes/vicPac1/jkStuff/vicPac1.11.ooc vicPac1.lift = no vicPac1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} vicPac1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} vicPac1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} vicPac1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} vicPac1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} vicPac1.refseq.mrna.native.load = no vicPac1.refseq.mrna.xeno.load = yes vicPac1.genbank.mrna.native.load = no vicPac1.genbank.mrna.xeno.load = no vicPac1.genbank.est.native.load = yes vicPac1.downloadDir = vicPac1 vicPac1.perChromTables = no # caePb2 (C. brenneri) caePb2.serverGenome = /hive/data/genomes/caePb2/caePb2.2bit caePb2.clusterGenome = /scratch/data/caePb2/caePb2.2bit caePb2.ooc = /scratch/data/caePb2/11.ooc caePb2.lift = /hive/data/genomes/caePb2/jkStuff/caePb2.supercontigs.lift caePb2.align.unplacedChroms = chrUn caePb2.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} caePb2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} caePb2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} caePb2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} caePb2.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} caePb2.refseq.mrna.native.load = no caePb2.refseq.mrna.xeno.load = yes caePb2.refseq.mrna.xeno.loadDesc = yes caePb2.genbank.mrna.xeno.load = yes caePb2.genbank.est.native.load = yes caePb2.genbank.est.native.loadDesc = no caePb2.downloadDir = caePb2 caePb2.perChromTables = no # caePb1 (C. brenneri aka C. PB2801) caePb1.serverGenome = /hive/data/genomes/caePb1/caePb1.2bit caePb1.clusterGenome = /scratch/data/caePb1/caePb1.2bit caePb1.ooc = /scratch/data/caePb1/11.ooc caePb1.lift = /hive/data/genomes/caePb1/jkStuff/caePb1.supercontigs.lift caePb1.align.unplacedChroms = chrUn caePb1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} caePb1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} caePb1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} caePb1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} caePb1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} caePb1.refseq.mrna.native.load = no caePb1.refseq.mrna.xeno.load = yes caePb1.refseq.mrna.xeno.loadDesc = yes caePb1.genbank.mrna.xeno.load = yes caePb1.genbank.est.native.load = no caePb1.genbank.est.native.loadDesc = no caePb1.downloadDir = caePb1 caePb1.perChromTables = no # caeRem3 (C. remanei) caeRem3.serverGenome = /hive/data/genomes/caeRem3/caeRem3.2bit caeRem3.clusterGenome = /scratch/data/caeRem3/caeRem3.2bit caeRem3.ooc = /scratch/data/caeRem3/11.ooc caeRem3.lift = /hive/data/genomes/caeRem3/downloads/caeRem3.chrUn.lift caeRem3.align.unplacedChroms = chrUn caeRem3.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} caeRem3.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} caeRem3.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} caeRem3.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} caeRem3.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} caeRem3.refseq.mrna.native.load = no caeRem3.refseq.mrna.xeno.load = yes caeRem3.refseq.mrna.xeno.loadDesc = yes caeRem3.genbank.mrna.xeno.load = yes caeRem3.genbank.est.native.load = yes caeRem3.genbank.est.native.loadDesc = no caeRem3.downloadDir = caeRem3 caeRem3.perChromTables = no # caeRem2 (C. remanei) caeRem2.serverGenome = /hive/data/genomes/caeRem2/caeRem2.2bit caeRem2.clusterGenome = /scratch/data/caeRem2/caeRem2.2bit caeRem2.ooc = /scratch/data/caeRem2/11.ooc caeRem2.lift = /hive/data/genomes/caeRem2/jkStuff/caeRem2.chrUn.lift caeRem2.align.unplacedChroms = chrUn caeRem2.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} caeRem2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} caeRem2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} caeRem2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} caeRem2.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} caeRem2.refseq.mrna.native.load = no caeRem2.refseq.mrna.xeno.load = yes caeRem2.refseq.mrna.xeno.loadDesc = yes caeRem2.genbank.mrna.xeno.load = yes caeRem2.genbank.est.native.load = yes caeRem2.genbank.est.native.loadDesc = no caeRem2.downloadDir = caeRem2 caeRem2.perChromTables = no # caeJap1 (C. japonica) caeJap1.serverGenome = /hive/data/genomes/caeJap1/caeJap1.2bit caeJap1.clusterGenome = /scratch/data/caeJap1/caeJap1.2bit caeJap1.ooc = /scratch/data/caeJap1/11.ooc caeJap1.lift = /hive/data/genomes/caeJap1/jkStuff/caeJap1.chrUn.lift caeJap1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} caeJap1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} caeJap1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} caeJap1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} caeJap1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} caeJap1.refseq.mrna.native.load = yes caeJap1.refseq.mrna.xeno.load = yes caeJap1.refseq.mrna.xeno.loadDesc = yes caeJap1.genbank.mrna.xeno.load = yes caeJap1.genbank.est.native.load = yes caeJap1.genbank.est.native.loadDesc = no caeJap1.downloadDir = caeJap1 caeJap1.perChromTables = no # Marmoset calJac3.serverGenome = /hive/data/genomes/calJac3/calJac3.2bit calJac3.clusterGenome = /scratch/data/calJac3/calJac3.2bit calJac3.ooc = /scratch/data/calJac3/calJac3.11.ooc calJac3.lift = no calJac3.perChromTables = no calJac3.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} calJac3.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} calJac3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} calJac3.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} calJac3.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} calJac3.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} calJac3.downloadDir = calJac3 calJac3.refseq.mrna.native.load = yes calJac3.refseq.mrna.xeno.load = yes calJac3.refseq.mrna.xeno.loadDesc = yes calJac3.genbank.mrna.xeno.load = yes calJac3.upstreamGeneTbl = ensGene calJac3.upstreamMaf = multiz13way /hive/data/genomes/calJac3/bed/multiz13way/species.list # Marmoset calJac1.serverGenome = /hive/data/genomes/calJac1/calJac1.2bit calJac1.clusterGenome = /scratch/data/calJac1/calJac1.2bit calJac1.ooc = /scratch/data/calJac1/11.ooc calJac1.lift = no calJac1.perChromTables = no calJac1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} calJac1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} calJac1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} calJac1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} calJac1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} calJac1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} calJac1.downloadDir = calJac1 calJac1.refseq.mrna.native.load = yes calJac1.refseq.mrna.xeno.load = yes calJac1.refseq.mrna.xeno.loadDesc = yes calJac1.genbank.mrna.xeno.load = yes calJac1.upstreamGeneTbl = xenoRefGene calJac1.upstreamMaf = multiz9way /hive/data/genomes/calJac1/bed/multiz9way/species.list # danRer3 (zebrafish) # Lift file partitions unplaced sequence pseudo-chroms danRer3.serverGenome = /hive/data/genomes/danRer3/danRer3.2bit danRer3.clusterGenome = /scratch/data/danRer3/danRer3.2bit danRer3.ooc = /scratch/data/danRer3/danRer3_11.ooc danRer3.align.unplacedChroms = chrNA,chrUn danRer3.lift = /hive/data/genomes/danRer3/liftSupertoChrom/liftNAandUnScaffoldsToChrom.lft danRer3.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} danRer3.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} danRer3.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} danRer3.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} danRer3.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} danRer3.genbank.mrna.xeno.load = yes danRer3.downloadDir = danRer3 danRer3.mgc = yes danRer3.upstreamGeneTbl = refGene danRer3.upstreamMaf = multiz5way /hive/data/genomes/danRer3/bed/multiz5way/species.list # danRer4 (zebrafish) # Lift file partitions unplaced sequence pseudo-chroms danRer4.serverGenome = /hive/data/genomes/danRer4/danRer4.2bit danRer4.clusterGenome = /scratch/data/danRer4/danRer4.2bit danRer4.ooc = /scratch/data/danRer4/danRer4_11.ooc danRer4.lift = /hive/data/genomes/danRer4/jkStuff/liftAll.lft danRer4.align.unplacedChroms = chrNA_random,chrUn_random danRer4.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} danRer4.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} danRer4.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} danRer4.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} danRer4.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} danRer4.genbank.mrna.xeno.load = yes danRer4.downloadDir = danRer4 danRer4.mgc = yes danRer4.upstreamGeneTbl = refGene danRer4.upstreamMaf = multiz7way /hive/data/genomes/danRer4/bed/multiz7way/species.lst # danRer5 (zebrafish) danRer5.serverGenome = /hive/data/genomes/danRer5/danRer5.2bit danRer5.clusterGenome = /scratch/data/danRer5/danRer5.2bit danRer5.ooc = /scratch/data/danRer5/danRer5_11.ooc danRer5.lift = /hive/data/genomes/danRer5/jkStuff/nonBridgedGap.lft danRer5.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} danRer5.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} danRer5.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} danRer5.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} danRer5.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} danRer5.genbank.mrna.xeno.load = yes danRer5.downloadDir = danRer5 danRer5.perChromTables = no danRer5.mgc = yes danRer5.orfeome = yes danRer5.upstreamGeneTbl = refGene # danRer6 (zebrafish) danRer6.serverGenome = /hive/data/genomes/danRer6/danRer6.2bit danRer6.clusterGenome = /scratch/data/danRer6/danRer6.2bit danRer6.ooc = /scratch/data/danRer6/11.ooc danRer6.lift = /hive/data/genomes/danRer6/jkStuff/danRer6.unBridged.lift danRer6.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} danRer6.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} danRer6.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} danRer6.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} danRer6.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} danRer6.genbank.mrna.xeno.load = yes danRer6.downloadDir = danRer6 danRer6.perChromTables = no danRer6.refseq.mrna.xeno.load = yes danRer6.mgc = yes danRer6.orfeome = yes danRer6.upstreamGeneTbl = refGene danRer6.upstreamMaf = multiz6way /hive/data/genomes/danRer6/bed/multiz6way/species.lst # danRer7 (zebrafish) danRer7.serverGenome = /hive/data/genomes/danRer7/danRer7.2bit danRer7.clusterGenome = /scratch/data/danRer7/danRer7.2bit danRer7.ooc = /scratch/data/danRer7/danRer7.11.ooc danRer7.lift = no danRer7.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} danRer7.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} danRer7.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} danRer7.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} danRer7.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} danRer7.genbank.mrna.xeno.load = yes danRer7.downloadDir = danRer7 danRer7.perChromTables = no danRer7.refseq.mrna.xeno.load = yes danRer7.mgc = yes danRer7.orfeome = yes danRer7.upstreamGeneTbl = ensGene danRer7.upstreamMaf = multiz8way /hive/data/genomes/danRer7/bed/multiz8way/species.lst # ci1 (ciona intestinalis) ci1.serverGenome = /hive/data/genomes/ci1/nib/Scaffold*.nib ci1.clusterGenome = /scratch/data/ci1/nib/Scaffold*.nib ci1.ooc = no ci1.maxIntron = 20000 ci1.lift = no ci1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} ci1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} ci1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} ci1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} ci1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} ci1.refseq.mrna.native.load = yes ci1.refseq.mrna.xeno.load = yes ci1.genbank.mrna.xeno.load = yes ci1.downloadDir = ci1 ci1.perChromTables = no # ci2 (ciona intestinalis) ci2.serverGenome = /hive/data/genomes/ci2/ci2.2bit ci2.clusterGenome = /scratch/data/ci2/ci2.2bit ci2.ooc = /scratch/data/ci2/11.ooc ci2.maxIntron = 20000 ci2.lift = no ci2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} ci2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} ci2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} ci2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} ci2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} ci2.refseq.mrna.native.load = yes ci2.refseq.mrna.xeno.load = yes ci2.genbank.mrna.xeno.load = yes ci2.downloadDir = ci2 ci2.perChromTables = no # strPur1 (S. purpuratus) # 302 genbank mRNA # 219 refseq mRNA # 89289 genbank EST strPur1.serverGenome = /hive/data/genomes/strPur1/strPur1.2bit strPur1.clusterGenome = /scratch/data/strPur1/strPur1.2bit strPur1.ooc = /scratch/data/strPur1/11.ooc strPur1.lift = no strPur1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} strPur1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} strPur1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} strPur1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} strPur1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} strPur1.refseq.mrna.native.load = yes strPur1.refseq.mrna.xeno.load = yes strPur1.genbank.mrna.xeno.load = yes strPur1.genbank.est.native.load = no strPur1.downloadDir = strPur1 strPur1.perChromTables = no # strPur2 (S. purpuratus) strPur2.serverGenome = /hive/data/genomes/strPur2/strPur2.2bit strPur2.clusterGenome = /scratch/data/strPur2/strPur2.2bit strPur2.ooc = /scratch/data/strPur2/11.ooc strPur2.lift = no strPur2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} strPur2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} strPur2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} strPur2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} strPur2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} strPur2.refseq.mrna.native.load = yes strPur2.refseq.mrna.xeno.load = yes strPur2.genbank.mrna.xeno.load = yes strPur2.genbank.est.native.load = yes strPur2.downloadDir = strPur2 strPur2.perChromTables = no # strPur4 (S. purpuratus) strPur4.serverGenome = /hive/data/genomes/strPur4/strPur4.2bit strPur4.clusterGenome = /scratch/data/strPur4/strPur4.2bit strPur4.ooc = /scratch/data/strPur4/strPur4.11.ooc strPur4.lift = no strPur4.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} strPur4.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} strPur4.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} strPur4.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} strPur4.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} strPur4.refseq.mrna.native.load = yes strPur4.refseq.mrna.xeno.load = yes strPur4.genbank.mrna.xeno.load = yes strPur4.genbank.est.native.load = yes strPur4.downloadDir = strPur4 strPur4.perChromTables = no # canFam1 (dog) canFam1.serverGenome = /hive/data/genomes/canFam1/nib/chr*.nib canFam1.clusterGenome = /scratch/data/canFam1/nib/chr*.nib canFam1.ooc = /scratch/data/canFam1/11.ooc canFam1.align.unplacedChroms = chrUn canFam1.lift = /hive/data/genomes/canFam1/jkStuff/liftAll.lft canFam1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} canFam1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} canFam1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} canFam1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} canFam1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} canFam1.refseq.mrna.native.load = yes canFam1.refseq.mrna.xeno.load = yes canFam1.genbank.mrna.xeno.load = yes canFam1.downloadDir = canFam1 canFam1.upstreamGeneTbl = ensGene # canFam2 (dog) canFam2.serverGenome = /hive/data/genomes/canFam2/nib/chr*.nib canFam2.clusterGenome = /scratch/data/canFam2/nib/chr*.nib canFam2.ooc = /scratch/data/canFam2/11.ooc canFam2.lift = /hive/data/genomes/canFam2/jkStuff/liftAll.lft canFam2.align.unplacedChroms = chrUn canFam2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} canFam2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} canFam2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} canFam2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} canFam2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} canFam2.refseq.mrna.native.load = yes canFam2.refseq.mrna.xeno.load = yes canFam2.genbank.mrna.xeno.load = yes canFam2.downloadDir = canFam2 canFam2.upstreamGeneTbl = ensGene # canFam3 (dog) canFam3.serverGenome = /hive/data/genomes/canFam3/canFam3.2bit canFam3.clusterGenome = /hive/data/genomes/canFam3/canFam3.2bit canFam3.ooc = /hive/data/genomes/canFam3/jkStuff/canFam3.11.ooc canFam3.lift = /hive/data/genomes/canFam3/jkStuff/canFam3.nonBridged.lift canFam3.align.unplacedChroms = chr* canFam3.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} canFam3.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} canFam3.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} canFam3.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} canFam3.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} canFam3.refseq.mrna.native.load = yes canFam3.refseq.mrna.xeno.load = yes canFam3.genbank.mrna.xeno.load = yes canFam3.downloadDir = canFam3 canFam3.upstreamGeneTbl = refGene canFam3.perChromTables = no # ailMel1 (panda) ailMel1.serverGenome = /hive/data/genomes/ailMel1/ailMel1.2bit ailMel1.clusterGenome = /scratch/data/ailMel1/ailMel1.2bit ailMel1.lift = no ailMel1.ooc = /scratch/data/ailMel1/ailMel1.11.ooc ailMel1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} ailMel1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} ailMel1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} ailMel1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} ailMel1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} ailMel1.refseq.mrna.native.load = no ailMel1.refseq.mrna.xeno.load = yes ailMel1.genbank.mrna.xeno.load = yes ailMel1.downloadDir = ailMel1 ailMel1.perChromTables = no ailMel1.upstreamGeneTbl = ensGene # droYak1 (D. yakuba) droYak1.serverGenome = /hive/data/genomes/droYak1/nib/chr*.nib droYak1.clusterGenome = /scratch/data/droYak1/nib/chr*.nib droYak1.ooc = /scratch/data/droYak1/11.ooc droYak1.lift = /hive/data/genomes/droYak1/jkStuff/liftAll.lft droYak1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} droYak1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} droYak1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} droYak1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} droYak1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} droYak1.refseq.mrna.native.load = no droYak1.refseq.mrna.xeno.load = yes droYak1.genbank.mrna.xeno.load = yes droYak1.downloadDir = droYak1 # anoGam1 (A. gambiae) anoGam1.serverGenome = /hive/data/genomes/anoGam1/nib/chr*.nib anoGam1.clusterGenome = /scratch/data/anoGam1/nib/chr*.nib anoGam1.ooc = /scratch/data/anoGam1/11.ooc anoGam1.lift = /hive/data/genomes/anoGam1/jkStuff/liftAll.lft anoGam1.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} anoGam1.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} anoGam1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} anoGam1.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} anoGam1.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} anoGam1.refseq.mrna.native.load = no anoGam1.genbank.mrna.xeno.load = yes anoGam1.downloadDir = anoGam1 # dp2 (D. pseudoobscura) dp2.serverGenome = /hive/data/genomes/dp2/nib/*.nib dp2.clusterGenome = /scratch/data/dp2/nib/*.nib dp2.ooc = /scratch/data/dp2/11.ooc dp2.lift = no dp2.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} dp2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} dp2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} dp2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} dp2.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} dp2.refseq.mrna.native.load = no dp2.refseq.mrna.xeno.load = yes dp2.genbank.mrna.xeno.load = yes dp2.downloadDir = dp2 dp2.perChromTables = no # dp3 (D. pseudoobscura) dp3.serverGenome = /hive/data/genomes/dp3/nib/*.nib dp3.clusterGenome = /scratch/data/dp3/nib/*.nib dp3.ooc = /scratch/data/dp3/11.ooc dp3.lift = /hive/data/genomes/dp3/jkStuff/liftAll.lft dp3.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} dp3.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} dp3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} dp3.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} dp3.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} dp3.refseq.mrna.native.load = no dp3.refseq.mrna.xeno.load = yes dp3.genbank.mrna.xeno.load = yes dp3.genbank.est.native.load = yes dp3.downloadDir = dp3 # tetNig2 (Tetraodon) tetNig2.serverGenome = /hive/data/genomes/tetNig2/tetNig2.2bit tetNig2.clusterGenome = /scratch/data/tetNig2/tetNig2.2bit tetNig2.ooc = /scratch/data/tetNig2/tetNig2.11.ooc tetNig2.lift = /scratch/data/tetNig2/tetNig2.contigs.lift tetNig2.align.unplacedChroms = chr*_random tetNig2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} tetNig2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} tetNig2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} tetNig2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} tetNig2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} tetNig2.downloadDir = tetNig2 tetNig2.genbank.est.native.load = no tetNig2.genbank.mrna.xeno.loadDesc = yes tetNig2.genbank.mrna.xeno.load = yes tetNig2.refseq.mrna.native.load = no tetNig2.upstreamGeneTbl = ensGene # tetNig1 (Tetraodon) tetNig1.serverGenome = /hive/data/genomes/tetNig1/nib/chr*.nib tetNig1.clusterGenome = /scratch/data/tetNig1/nib/chr*.nib tetNig1.ooc = /scratch/data/tetNig1/11.ooc tetNig1.lift = /hive/data/genomes/tetNig1/jkStuff/liftAll.lft tetNig1.align.unplacedChroms = chrUn_random tetNig1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} tetNig1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} tetNig1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} tetNig1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} tetNig1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} tetNig1.downloadDir = tetNig1 tetNig1.genbank.est.native.load = no tetNig1.genbank.mrna.xeno.loadDesc = yes tetNig1.genbank.mrna.xeno.load = yes tetNig1.refseq.mrna.native.load = no tetNig1.upstreamGeneTbl = ensGene # gasAcu1 (G. Aculeatus) gasAcu1.serverGenome = /hive/data/genomes/gasAcu1/gasAcu1.2bit gasAcu1.clusterGenome = /scratch/data/gasAcu1/gasAcu1.2bit gasAcu1.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} gasAcu1.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} gasAcu1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} gasAcu1.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} gasAcu1.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} gasAcu1.ooc = /scratch/data/gasAcu1/11.ooc gasAcu1.lift = /hive/data/genomes/gasAcu1/jkStuff/liftAll.lft gasAcu1.genbank.mrna.xeno.load = yes gasAcu1.downloadDir = gasAcu1 gasAcu1.upstreamGeneTbl = ensGene gasAcu1.upstreamMaf = multiz8way /hive/data/genomes/gasAcu1/bed/multiz8way/species.lst # chiLan1 (Chinchilla lanigera) chiLan1.serverGenome = /hive/data/genomes/chiLan1/chiLan1.2bit chiLan1.clusterGenome = /hive/data/genomes/chiLan1/chiLan1.2bit chiLan1.lift = no chiLan1.perChromTables = no chiLan1.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} chiLan1.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} chiLan1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} chiLan1.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} chiLan1.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} chiLan1.ooc = /hive/data/genomes/chiLan1/jkStuff/chiLan1.11.ooc chiLan1.refseq.mrna.native.load = yes chiLan1.refseq.mrna.xeno.load = yes chiLan1.genbank.mrna.xeno.load = no chiLan1.genbank.est.native.load = yes chiLan1.downloadDir = chiLan1 # musFur1 (Ferret, Mustela putorius furo, taxId 9669) musFur1.serverGenome = /hive/data/genomes/musFur1/musFur1.2bit musFur1.clusterGenome = /hive/data/genomes/musFur1/musFur1.2bit musFur1.ooc = /hive/data/genomes/musFur1/jkStuff/musFur1.11.ooc musFur1.lift = no musFur1.perChromTables = no musFur1.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} musFur1.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} musFur1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} musFur1.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} musFur1.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} musFur1.refseq.mrna.native.load = yes musFur1.refseq.mrna.xeno.load = yes musFur1.genbank.mrna.xeno.load = no musFur1.genbank.est.native.load = yes musFur1.downloadDir = musFur1 # oryLat2 (Oryzias latipes - Medaka) oryLat2.serverGenome = /hive/data/genomes/oryLat2/oryLat2.2bit oryLat2.clusterGenome = /scratch/data/oryLat2/oryLat2.2bit oryLat2.lift = /hive/data/genomes/oryLat2/jkStuff/liftAll.lft oryLat2.perChromTables = no oryLat2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} oryLat2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} oryLat2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} oryLat2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} oryLat2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} oryLat2.ooc = /scratch/data/oryLat2/11.ooc oryLat2.genbank.mrna.xeno.load = yes oryLat2.refseq.mrna.native.load = yes oryLat2.refseq.mrna.xeno.load = yes oryLat2.downloadDir = oryLat2 oryLat2.upstreamGeneTbl = ensGene oryLat2.upstreamMaf = multiz5way /hive/data/genomes/oryLat2/bed/multiz5way/species.list # oryLat1 (Oryzias latipes - Medaka) oryLat1.serverGenome = /hive/data/genomes/oryLat1/oryLat1.2bit oryLat1.clusterGenome = /scratch/data/oryLat1/oryLat1.2bit oryLat1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} oryLat1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} oryLat1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} oryLat1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} oryLat1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} oryLat1.ooc = /scratch/data/oryLat1/11.ooc oryLat1.lift = /hive/data/genomes/oryLat1/jkStuff/liftAll.lft oryLat1.genbank.mrna.xeno.load = yes oryLat1.refseq.mrna.native.load = no oryLat1.refseq.mrna.xeno.load = yes oryLat1.downloadDir = oryLat1 # oviAri1 (Sheep) oviAri1.serverGenome = /hive/data/genomes/oviAri1/oviAri1.2bit oviAri1.clusterGenome = /scratch/data/oviAri1/oviAri1.2bit oviAri1.ooc = /scratch/data/oviAri1/oviAri1.11.ooc oviAri1.lift = no oviAri1.perChromTables = no oviAri1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} oviAri1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} oviAri1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} oviAri1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} oviAri1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} oviAri1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} oviAri1.downloadDir = oviAri1 oviAri1.refseq.mrna.native.load = yes oviAri1.refseq.mrna.xeno.load = yes oviAri1.refseq.mrna.xeno.loadDesc = yes oviAri1.genbank.mrna.xeno.load = yes oviAri1.upstreamGeneTbl = refGene # otoGar3 (bushbaby) otoGar3.serverGenome = /hive/data/genomes/otoGar3/otoGar3.2bit otoGar3.clusterGenome = /hive/data/genomes/otoGar3/otoGar3.2bit otoGar3.ooc = /hive/data/genomes/otoGar3/jkStuff/otoGar3.11.ooc otoGar3.lift = no otoGar3.perChromTables = no otoGar3.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} otoGar3.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} otoGar3.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} otoGar3.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} otoGar3.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} otoGar3.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} otoGar3.downloadDir = otoGar3 otoGar3.refseq.mrna.native.load = no otoGar3.refseq.mrna.xeno.load = yes otoGar3.genbank.mrna.xeno.load = yes otoGar3.genbank.mrna.xeno.loadDesc = no otoGar3.genbank.est.native.load = no # susScr3 (pig) susScr3.serverGenome = /hive/data/genomes/susScr3/susScr3.2bit susScr3.clusterGenome = /hive/data/genomes/susScr3/susScr3.2bit susScr3.ooc = /hive/data/genomes/susScr3/jkStuff/susScr3.11.ooc susScr3.lift = /hive/data/genomes/susScr3/jkStuff/susScr3.nonBridged.lift susScr3.perChromTables = no susScr3.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} susScr3.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} susScr3.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} susScr3.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} susScr3.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} susScr3.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} susScr3.downloadDir = susScr3 susScr3.refseq.mrna.native.load = yes susScr3.refseq.mrna.xeno.load = yes susScr3.genbank.mrna.xeno.load = yes susScr3.genbank.mrna.xeno.loadDesc = no susScr3.genbank.est.native.load = yes # susScr3.upstreamGeneTbl = ensGene # susScr3.upstreamMaf = multiz12way # /hive/data/genomes/susScr3/bed/multiz12way/species.list # susScr2 (Pig) susScr2.serverGenome = /hive/data/genomes/susScr2/susScr2.2bit susScr2.clusterGenome = /scratch/data/susScr2/susScr2.2bit susScr2.ooc = /scratch/data/susScr2/susScr2.11.ooc susScr2.lift = /scratch/data/susScr2/susScr2.nonBridged.lft susScr2.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} susScr2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} susScr2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} susScr2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} susScr2.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} susScr2.downloadDir = susScr2 susScr2.genbank.mrna.xeno.loadDesc = yes susScr2.genbank.mrna.xeno.load = yes susScr2.refseq.mrna.native.load = no susScr2.upstreamGeneTbl = ensGene # equCab2 (Equus caballus) equCab2.serverGenome = /hive/data/genomes/equCab2/equCab2.2bit equCab2.clusterGenome = /scratch/data/equCab2/equCab2.2bit equCab2.ooc = /scratch/data/equCab2/equCab2.11.ooc equCab2.lift = /hive/data/genomes/equCab2/jkStuff/equCab2.chrUn.lift equCab2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} equCab2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} equCab2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} equCab2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} equCab2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} equCab2.align.unplacedChroms = chrUn equCab2.refseq.mrna.xeno.load = yes equCab2.genbank.mrna.xeno.load = yes equCab2.downloadDir = equCab2 equCab2.upstreamGeneTbl = refGene # equCab2.upstreamMaf = multiz6way /hive/data/genomes/equCab2/bed/multiz6way/species.list # equCab1 (Equus caballus) equCab1.serverGenome = /hive/data/genomes/equCab1/equCab1.2bit equCab1.clusterGenome = /scratch/data/equCab1/equCab1.2bit equCab1.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} equCab1.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} equCab1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} equCab1.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} equCab1.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} equCab1.ooc = /scratch/data/equCab1/11.ooc equCab1.lift = /hive/data/genomes/equCab1/jkStuff/genbank.lft equCab1.align.unplacedChroms = chrUn equCab1.genbank.mrna.xeno.load = yes equCab1.downloadDir = equCab1 equCab1.upstreamGeneTbl = refGene # cerSim1 (Ceratotherium simum - White Rhino) cerSim1.serverGenome = /hive/data/genomes/cerSim1/cerSim1.2bit cerSim1.clusterGenome = /hive/data/genomes/cerSim1/cerSim1.2bit cerSim1.ooc = /hive/data/genomes/cerSim1/jkStuff/cerSim1.11.ooc cerSim1.lift = no cerSim1.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} cerSim1.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} cerSim1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} cerSim1.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} cerSim1.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} cerSim1.refseq.mrna.native.load = no cerSim1.refseq.mrna.xeno.load = yes cerSim1.genbank.mrna.xeno.load = no cerSim1.genbank.est.native.load = no cerSim1.downloadDir = cerSim1 cerSim1.perChromTables = no # felCat5 felCat5.serverGenome = /hive/data/genomes/felCat5/felCat5.2bit felCat5.clusterGenome = /hive/data/genomes/felCat5/felCat5.2bit felCat5.ooc = /hive/data/genomes/felCat5/jkStuff/felCat5.11.ooc felCat5.lift = /hive/data/genomes/felCat5/jkStuff/felCat5.nonBridged.lift felCat5.perChromTables = no felCat5.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} felCat5.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} felCat5.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} felCat5.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} felCat5.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} felCat5.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} felCat5.genbank.mrna.xeno.load = yes felCat5.downloadDir = felCat5 felCat5.refseq.mrna.native.load = yes felCat5.refseq.mrna.xeno.load = yes felCat5.refseq.mrna.xeno.loadDesc = yes # felCat5.upstreamGeneTbl = refGene # felCat5.upstreamMaf = multiz6way /hive/data/genomes/felCat5/bed/multiz6way/species.list # felCat4 felCat4.serverGenome = /hive/data/genomes/felCat4/felCat4.2bit felCat4.clusterGenome = /scratch/data/felCat4/felCat4.2bit felCat4.ooc = /scratch/data/felCat4/felCat4.11.ooc felCat4.lift = no felCat4.perChromTables = no felCat4.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} felCat4.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} felCat4.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} felCat4.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} felCat4.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} felCat4.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} felCat4.genbank.mrna.xeno.load = yes felCat4.downloadDir = felCat4 felCat4.refseq.mrna.native.load = yes felCat4.refseq.mrna.xeno.load = yes felCat4.refseq.mrna.xeno.loadDesc = yes felCat4.upstreamGeneTbl = refGene felCat4.upstreamMaf = multiz6way /hive/data/genomes/felCat4/bed/multiz6way/species.list # felCat3 (cat) 217790 scaffolds felCat3.serverGenome = /hive/data/genomes/felCat3/felCat3.2bit felCat3.clusterGenome = /scratch/data/felCat3/felCat3.2bit felCat3.ooc = /scratch/data/felCat3/11.ooc felCat3.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} felCat3.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} felCat3.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} felCat3.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} felCat3.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} felCat3.genbank.mrna.xeno.load = yes felCat3.lift = no felCat3.refseq.mrna.xeno.load = yes felCat3.downloadDir = felCat3 felCat3.perChromTables = no felCat3.upstreamGeneTbl = ensGene felCat3.upstreamMaf = multiz4way /hive/data/genomes/felCat3/bed/multiz4way/species.lst # bosTau2 (B. taurus) 30 chromosomes plus 98058 scaffolds # Lift file partitions unplaced sequence pseudo-chroms bosTau2.serverGenome = /hive/data/genomes/bosTau2/bosTau2.2bit bosTau2.clusterGenome = /scratch/data/bosTau2/bosTau2.2bit bosTau2.ooc = /scratch/data/bosTau2/11.ooc bosTau2.lift = /hive/data/genomes/bosTau2/downloads/chrBin0.lft bosTau2.align.unplacedChroms = chrBin0 bosTau2.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} bosTau2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} bosTau2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} bosTau2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} bosTau2.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} bosTau2.refseq.mrna.native.load = yes bosTau2.refseq.mrna.xeno.load = yes bosTau2.genbank.mrna.xeno.load = no bosTau2.downloadDir = bosTau2 bosTau2.perChromTables = no bosTau2.mgc = yes bosTau2.upstreamGeneTbl = refGene # bosTau3 (B. taurus) 30 chromosomes plus 13045 scaffolds bosTau3.serverGenome = /hive/data/genomes/bosTau3/bosTau3.2bit bosTau3.clusterGenome = /scratch/data/bosTau3/bosTau3.2bit bosTau3.ooc = /scratch/data/bosTau3/11.ooc bosTau3.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} bosTau3.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} bosTau3.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} bosTau3.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} bosTau3.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} bosTau3.genbank.mrna.xeno.load = yes bosTau3.lift = no bosTau3.downloadDir = bosTau3 bosTau3.perChromTables = no bosTau3.mgc = yes bosTau3.upstreamGeneTbl = refGene # bosTau4 (B. taurus) 31 chromosomes plus 11869 scaffolds bosTau4.serverGenome = /hive/data/genomes/bosTau4/bosTau4.2bit bosTau4.clusterGenome = /scratch/data/bosTau4/bosTau4.2bit bosTau4.ooc = /scratch/data/bosTau4/bosTau4.11.ooc bosTau4.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} bosTau4.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} bosTau4.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} bosTau4.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} bosTau4.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} bosTau4.genbank.mrna.xeno.load = yes bosTau4.lift = no bosTau4.downloadDir = bosTau4 bosTau4.perChromTables = no bosTau4.mgc = yes bosTau4.upstreamGeneTbl = mgcGenes bosTau4.upstreamMaf = multiz5way /hive/data/genomes/bosTau4/bed/multiz5way/species.list # bosTau6 (Cow) bosTau6.serverGenome = /hive/data/genomes/bosTau6/bosTau6.2bit bosTau6.clusterGenome = /scratch/data/bosTau6/bosTau6.2bit bosTau6.ooc = /scratch/data/bosTau6/bosTau6.11.ooc bosTau6.lift = no bosTau6.perChromTables = no bosTau6.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} bosTau6.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} bosTau6.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} bosTau6.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} bosTau6.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} bosTau6.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} bosTau6.downloadDir = bosTau6 bosTau6.refseq.mrna.native.load = yes bosTau6.refseq.mrna.xeno.load = yes bosTau6.refseq.mrna.xeno.loadDesc = yes bosTau6.genbank.mrna.xeno.load = yes bosTau6.upstreamGeneTbl = refGene # bosTau7 (Cow) bosTau7.serverGenome = /hive/data/genomes/bosTau7/bosTau7.2bit bosTau7.clusterGenome = /scratch/data/bosTau7/bosTau7.2bit bosTau7.ooc = /scratch/data/bosTau7/bosTau7.11.ooc bosTau7.lift = no bosTau7.perChromTables = no bosTau7.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} bosTau7.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} bosTau7.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} bosTau7.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} bosTau7.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} bosTau7.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} bosTau7.downloadDir = bosTau7 bosTau7.refseq.mrna.native.load = yes bosTau7.refseq.mrna.xeno.load = yes bosTau7.refseq.mrna.xeno.loadDesc = yes bosTau7.genbank.mrna.xeno.load = yes bosTau7.upstreamGeneTbl = refGene # xenTro3 (X. tropicalis) 19550 scaffolds xenTro3.serverGenome = /hive/data/genomes/xenTro3/xenTro3.2bit xenTro3.clusterGenome = /scratch/data/xenTro3/xenTro3.2bit xenTro3.ooc = /scratch/data/xenTro3/xenTro3.11.ooc xenTro3.lift = no xenTro3.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} xenTro3.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} xenTro3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} xenTro3.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} xenTro3.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} xenTro3.refseq.mrna.native.load = yes xenTro3.genbank.est.native.load = yes xenTro3.refseq.mrna.xeno.load = no xenTro3.genbank.mrna.xeno.load = no xenTro3.downloadDir = xenTro3 xenTro3.perChromTables = no xenTro3.mgc = yes xenTro3.upstreamGeneTbl = ensGene xenTro3.upstreamMaf = multiz9way /hive/data/genomes/xenTro3/bed/multiz9way/species.list # xenTro2 (X. tropicalis) 19579 scaffolds xenTro2.serverGenome = /hive/data/genomes/xenTro2/xenTro2.2bit xenTro2.clusterGenome = /scratch/data/xenTro2/xenTro2.2bit xenTro2.ooc = /scratch/data/xenTro2/11.ooc xenTro2.lift = no xenTro2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} xenTro2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} xenTro2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} xenTro2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} xenTro2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} xenTro2.refseq.mrna.native.load = yes xenTro2.genbank.mrna.xeno.load = no xenTro2.downloadDir = xenTro2 xenTro2.perChromTables = no xenTro2.mgc = yes xenTro2.upstreamGeneTbl = mgcGenes xenTro2.upstreamMaf = multiz7way /hive/data/genomes/xenTro2/bed/multiz7way/species.lst # xenTro1 (X. tropicalis) 27064 scaffolds! xenTro1.serverGenome = /hive/data/genomes/xenTro1/xenTro1.2bit xenTro1.clusterGenome = /scratch/data/xenTro1/xenTro1.2bit xenTro1.ooc = /scratch/data/xenTro1/11.ooc xenTro1.lift = no xenTro1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} xenTro1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} xenTro1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} xenTro1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} xenTro1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} xenTro1.refseq.mrna.native.load = no xenTro1.genbank.mrna.xeno.load = no xenTro1.downloadDir = xenTro1 xenTro1.perChromTables = no xenTro1.mgc = yes xenTro1.upstreamGeneTbl = mgcGenes # anoCar2 (A. carolinensis) anoCar2.serverGenome = /hive/data/genomes/anoCar2/anoCar2.2bit anoCar2.clusterGenome = /scratch/data/anoCar2/anoCar2.2bit anoCar2.ooc = /scratch/data/anoCar2/anoCar2.11.ooc anoCar2.lift = /scratch/data/anoCar2/nonBridged.lift anoCar2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} anoCar2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} anoCar2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} anoCar2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} anoCar2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} anoCar2.refseq.mrna.native.load = no anoCar2.genbank.est.native.load = yes anoCar2.refseq.mrna.xeno.load = yes anoCar2.genbank.mrna.xeno.load = yes anoCar2.downloadDir = anoCar2 anoCar2.perChromTables = no anoCar2.upstreamGeneTbl = ensGene anoCar2.upstreamMaf = multiz7way /hive/data/genomes/anoCar2/bed/multiz7way/species.list # anoCar1 (A. carolinensis) anoCar1.serverGenome = /hive/data/genomes/anoCar1/anoCar1.2bit anoCar1.clusterGenome = /scratch/data/anoCar1/anoCar1.2bit anoCar1.ooc = /scratch/data/anoCar1/11.ooc anoCar1.lift = no anoCar1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} anoCar1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} anoCar1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} anoCar1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} anoCar1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} anoCar1.refseq.mrna.native.load = no anoCar1.genbank.est.native.load = no anoCar1.refseq.mrna.xeno.load = yes anoCar1.genbank.mrna.xeno.load = yes anoCar1.downloadDir = anoCar1 anoCar1.perChromTables = no anoCar1.upstreamGeneTbl = ensGene # macEug1 (wallaby) macEug1.serverGenome = /hive/data/genomes/macEug1/macEug1.2bit macEug1.clusterGenome = /scratch/data/macEug1/macEug1.2bit macEug1.ooc = /scratch/data/macEug1/macEug1.11.ooc macEug1.lift = no macEug1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} macEug1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} macEug1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} macEug1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} macEug1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} macEug1.refseq.mrna.native.load = no macEug1.refseq.mrna.xeno.load = yes macEug1.genbank.mrna.xeno.load = yes macEug1.genbank.est.native.load = no macEug1.downloadDir = macEug1 macEug1.perChromTables = no macEug1.upstreamGeneTbl = xenoRefGene # macEug2 (wallaby) macEug2.serverGenome = /hive/data/genomes/macEug2/macEug2.2bit macEug2.clusterGenome = /scratch/data/macEug2/macEug2.2bit macEug2.ooc = /scratch/data/macEug2/macEug2.11.ooc macEug2.lift = no macEug2.perChromTables = no macEug2.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} macEug2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} macEug2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} macEug2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} macEug2.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} macEug2.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} macEug2.downloadDir = macEug2 macEug2.refseq.mrna.native.load = no macEug2.refseq.mrna.xeno.load = yes macEug2.refseq.mrna.xeno.loadDesc = yes macEug2.genbank.est.native.load = yes macEug2.genbank.est.native.loadDesc = yes macEug2.genbank.mrna.native.load = yes macEug2.genbank.mrna.native.loadDesc = yes macEug2.genbank.mrna.xeno.load = yes macEug2.genbank.mrna.xeno.loadDesc = yes macEug2.genbank.est.native.load = yes macEug2.genbank.est.native.loadDesc = yes # triMan1 (manatee) triMan1.serverGenome = /hive/data/genomes/triMan1/triMan1.2bit triMan1.clusterGenome = /hive/data/genomes/triMan1/triMan1.2bit triMan1.ooc = /hive/data/genomes/triMan1/jkStuff/triMan1.11.ooc triMan1.lift = no triMan1.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} triMan1.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} triMan1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} triMan1.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} triMan1.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} triMan1.refseq.mrna.native.load = no triMan1.refseq.mrna.xeno.load = yes triMan1.genbank.mrna.xeno.load = yes triMan1.genbank.est.native.load = no triMan1.downloadDir = triMan1 triMan1.perChromTables = no # dasNov1 (armadillo) dasNov1.serverGenome = /hive/data/genomes/dasNov1/dasNov1.2bit dasNov1.clusterGenome = /scratch/data/dasNov1/dasNov1.2bit dasNov1.ooc = /scratch/data/dasNov1/11.ooc dasNov1.lift = no dasNov1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} dasNov1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} dasNov1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} dasNov1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} dasNov1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} dasNov1.refseq.mrna.native.load = no dasNov1.refseq.mrna.xeno.load = yes dasNov1.genbank.mrna.xeno.load = yes dasNov1.genbank.est.native.load = no dasNov1.downloadDir = dasNov1 dasNov1.perChromTables = no # loxAfr3 (elephant) loxAfr3.serverGenome = /hive/data/genomes/loxAfr3/loxAfr3.2bit loxAfr3.clusterGenome = /scratch/data/loxAfr3/loxAfr3.2bit loxAfr3.ooc = /scratch/data/loxAfr3/loxAfr3.11.ooc loxAfr3.lift = no loxAfr3.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} loxAfr3.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} loxAfr3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} loxAfr3.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} loxAfr3.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} loxAfr3.refseq.mrna.native.load = yes loxAfr3.refseq.mrna.xeno.load = yes loxAfr3.genbank.mrna.xeno.load = yes loxAfr3.genbank.est.native.load = no loxAfr3.downloadDir = loxAfr3 loxAfr3.perChromTables = no loxAfr3.upstreamGeneTbl = ensGene # loxAfr1 (elephant) loxAfr1.serverGenome = /hive/data/genomes/loxAfr1/loxAfr1.2bit loxAfr1.clusterGenome = /scratch/data/loxAfr1/loxAfr1.2bit loxAfr1.ooc = /scratch/data/loxAfr1/11.ooc loxAfr1.lift = no loxAfr1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} loxAfr1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} loxAfr1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} loxAfr1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} loxAfr1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} loxAfr1.refseq.mrna.native.load = no loxAfr1.refseq.mrna.xeno.load = yes loxAfr1.genbank.mrna.xeno.load = yes loxAfr1.genbank.est.native.load = no loxAfr1.downloadDir = loxAfr1 loxAfr1.perChromTables = no # echTel1 (tenrec) echTel1.serverGenome = /hive/data/genomes/echTel1/echTel1.2bit echTel1.clusterGenome = /scratch/data/echTel1/echTel1.2bit echTel1.ooc = /hive/data/genomes/echTel1/jkStuff/echTel1.11.ooc echTel1.lift = no echTel1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} echTel1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} echTel1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} echTel1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} echTel1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} echTel1.refseq.mrna.native.load = no echTel1.refseq.mrna.xeno.load = yes echTel1.genbank.mrna.xeno.load = no echTel1.genbank.est.native.load = no echTel1.genbank.mrna.native.load = no echTel1.genbank.mrna.native.loadDesc = no echTel1.downloadDir = echTel1 echTel1.perChromTables = no # oryCun2 (rabbit) oryCun2.serverGenome = /hive/data/genomes/oryCun2/oryCun2.2bit oryCun2.clusterGenome = /scratch/data/oryCun2/oryCun2.2bit oryCun2.ooc = /scratch/data/oryCun2/oryCun2.11.ooc oryCun2.lift = /scratch/data/oryCun2/oryCun2.contigs.lift oryCun2.perChromTables = no oryCun2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} oryCun2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} oryCun2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} oryCun2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} oryCun2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} oryCun2.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} oryCun2.downloadDir = oryCun2 oryCun2.refseq.mrna.native.load = yes oryCun2.refseq.mrna.xeno.load = yes oryCun2.refseq.mrna.xeno.loadDesc = yes oryCun2.genbank.mrna.xeno.load = yes oryCun2.upstreamGeneTbl = xenoRefGene # oryCun1 (rabbit) oryCun1.serverGenome = /hive/data/genomes/oryCun1/oryCun1.2bit oryCun1.clusterGenome = /scratch/data/oryCun1/oryCun1.2bit oryCun1.ooc = no oryCun1.lift = no oryCun1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} oryCun1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} oryCun1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} oryCun1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} oryCun1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} oryCun1.refseq.mrna.native.load = no oryCun1.refseq.mrna.xeno.load = yes oryCun1.genbank.mrna.xeno.load = yes oryCun1.genbank.est.native.load = yes oryCun1.downloadDir = oryCun1 oryCun1.perChromTables = no # cavPor3 (C. porcellus) 3144 scaffolds 967 are multi-contig and 2076 are single contig cavPor3.serverGenome = /hive/data/genomes/cavPor3/cavPor3.2bit cavPor3.clusterGenome = /scratch/data/cavPor3/cavPor3.2bit cavPor3.ooc = /scratch/data/cavPor3/cavPor3.11.ooc cavPor3.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} cavPor3.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} cavPor3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} cavPor3.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} cavPor3.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} cavPor3.lift = no cavPor3.downloadDir = cavPor3 cavPor3.perChromTables = no cavPor3.refseq.mrna.native.load = yes cavPor3.refseq.mrna.xeno.load = yes cavPor3.genbank.mrna.xeno.load = yes cavPor3.genbank.est.native.load = yes cavPor3.upstreamGeneTbl = xenoRefGene cavPor3.upstreamMaf = multiz8way /hive/data/genomes/cavPor3/bed/multiz8way/species.list # ornAna1 (Platypus -- O. anatinus) ornAna1.serverGenome = /hive/data/genomes/ornAna1/ornAna1.2bit ornAna1.clusterGenome = /scratch/data/ornAna1/ornAna1.2bit ornAna1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} ornAna1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} ornAna1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} ornAna1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} ornAna1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} ornAna1.ooc = /scratch/data/ornAna1/11.ooc ornAna1.lift = no ornAna1.refseq.mrna.xeno.load = yes ornAna1.refseq.mrna.xeno.loadDesc = yes ornAna1.genbank.mrna.xeno.load = yes ornAna1.downloadDir = ornAna1 ornAna1.perChromTables = no ornAna1.upstreamGeneTbl = ensGene ornAna1.upstreamMaf = multiz6way /hive/data/genomes/ornAna1/bed/multiz6way.2007-04-24/species.lst # petMar2 (Petromyzon marinus - Sea Lamprey) petMar2.serverGenome = /hive/data/genomes/petMar2/petMar2.2bit petMar2.clusterGenome = /hive/data/genomes/petMar2/petMar2.2bit petMar2.ooc = /hive/data/genomes/petMar2/jkStuff/petMar2.11.ooc petMar2.lift = no petMar2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} petMar2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} petMar2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} petMar2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} petMar2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} petMar2.refseq.mrna.native.load = yes petMar2.refseq.mrna.xeno.load = yes petMar2.genbank.mrna.xeno.load = no petMar2.genbank.est.native.load = yes petMar2.downloadDir = petMar2 petMar2.perChromTables = no # petMar1 (Petromyzon marinus - Sea Lamprey) petMar1.serverGenome = /hive/data/genomes/petMar1/petMar1.2bit petMar1.clusterGenome = /scratch/data/petMar1/petMar1.2bit petMar1.ooc = /scratch/data/petMar1/petMar1.11.ooc petMar1.lift = no petMar1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} petMar1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} petMar1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} petMar1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} petMar1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} petMar1.refseq.mrna.native.load = yes petMar1.refseq.mrna.xeno.load = yes petMar1.genbank.mrna.xeno.load = yes petMar1.genbank.est.native.load = yes petMar1.downloadDir = petMar1 petMar1.perChromTables = no petMar1.upstreamGeneTbl = xenoRefGene petMar1.upstreamMaf = multiz6way /hive/data/genomes/petMar1/bed/multiz6way/species.list # braFlo2 (Branchiostoma floridae - Lancelet) braFlo2.serverGenome = /hive/data/genomes/braFlo2/braFlo2.2bit braFlo2.clusterGenome = /hive/data/genomes/braFlo2/braFlo2.2bit braFlo2.ooc = /hive/data/genomes/braFlo2/jkStuff/braFlo2.11.ooc braFlo2.lift = /hive/data/genomes/braFlo2/jkStuff/braFlo2.nonBridged.lift braFlo2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} braFlo2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} braFlo2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} braFlo2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} braFlo2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} braFlo2.refseq.mrna.native.load = yes braFlo2.refseq.mrna.xeno.load = yes braFlo2.genbank.mrna.xeno.load = no braFlo2.genbank.est.native.load = yes braFlo2.downloadDir = braFlo2 braFlo2.perChromTables = no # braFlo1 (Branchiostoma floridae - Lancelet) braFlo1.serverGenome = /hive/data/genomes/braFlo1/braFlo1.2bit braFlo1.clusterGenome = /scratch/data/braFlo1/braFlo1.2bit braFlo1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} braFlo1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} braFlo1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} braFlo1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} braFlo1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} braFlo1.ooc = /scratch/data/braFlo1/11.ooc braFlo1.lift = /hive/data/genomes/braFlo1/jkStuff/liftAll.lft braFlo1.refseq.mrna.native.load = no braFlo1.refseq.mrna.xeno.load = yes braFlo1.genbank.mrna.xeno.load = yes braFlo1.genbank.est.native.load = yes braFlo1.downloadDir = braFlo1 braFlo1.perChromTables = no braFlo1.upstreamGeneTbl = xenoRefGene braFlo1.upstreamMaf = multiz5way /hive/data/genomes/braFlo1/bed/multiz5way/species.list # droAna1 (D. ananassae) droAna1.serverGenome = /hive/data/genomes/droAna1/droAna1.2bit droAna1.clusterGenome = /scratch/data/droAna1/droAna1.2bit droAna1.ooc = /scratch/data/droAna1/11.ooc droAna1.lift = no droAna1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} droAna1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} droAna1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} droAna1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} droAna1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} droAna1.refseq.mrna.native.load = no droAna1.refseq.mrna.xeno.load = yes droAna1.genbank.mrna.xeno.load = yes # GenBank has no D. ananassae ESTs at this point... that may change. droAna1.genbank.est.native.load = no droAna1.downloadDir = droAna1 droAna1.perChromTables = no # droAna2 (D. ananassae) droAna2.serverGenome = /hive/data/genomes/droAna2/droAna2.2bit droAna2.clusterGenome = /scratch/data/droAna2/droAna2.2bit droAna2.ooc = /scratch/data/droAna2/11.ooc droAna2.lift = no droAna2.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} droAna2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} droAna2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} droAna2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} droAna2.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} droAna2.refseq.mrna.native.load = no droAna2.refseq.mrna.xeno.load = yes droAna2.genbank.mrna.xeno.load = yes # GenBank has no D. ananassae ESTs at this point... that may change. droAna2.genbank.est.native.load = no droAna2.downloadDir = droAna2 droAna2.perChromTables = no # droMoj1 (D. mojavensis) droMoj1.serverGenome = /hive/data/genomes/droMoj1/droMoj1.2bit droMoj1.clusterGenome = /scratch/data/droMoj1/droMoj1.2bit droMoj1.ooc = /scratch/data/droMoj1/11.ooc droMoj1.lift = no droMoj1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} droMoj1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} droMoj1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} droMoj1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} droMoj1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} droMoj1.refseq.mrna.native.load = no droMoj1.refseq.mrna.xeno.load = yes droMoj1.genbank.mrna.xeno.load = yes # GenBank has no D. mojavensis ESTs at this point... that may change. droMoj1.genbank.est.native.load = no droMoj1.downloadDir = droMoj1 droMoj1.perChromTables = no # droMoj2 (D. mojavensis) # genbank has 1 mRNA and 0 ESTs at time of initial build droMoj2.serverGenome = /hive/data/genomes/droMoj2/droMoj2.2bit droMoj2.clusterGenome = /scratch/data/droMoj2/droMoj2.2bit droMoj2.ooc = /scratch/data/droMoj2/11.ooc droMoj2.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} droMoj2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} droMoj2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} droMoj2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} droMoj2.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} droMoj2.lift = no droMoj2.refseq.mrna.native.load = no droMoj2.refseq.mrna.xeno.load = yes droMoj2.genbank.mrna.xeno.load = yes droMoj2.genbank.est.native.load = no droMoj2.downloadDir = droMoj2 droMoj2.perChromTables = no # droVir1 (D. virilis) droVir1.serverGenome = /hive/data/genomes/droVir1/droVir1.2bit droVir1.clusterGenome = /scratch/data/droVir1/droVir1.2bit droVir1.ooc = /scratch/data/droVir1/11.ooc droVir1.lift = no droVir1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} droVir1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} droVir1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} droVir1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} droVir1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} droVir1.refseq.mrna.native.load = no droVir1.refseq.mrna.xeno.load = yes droVir1.genbank.mrna.xeno.load = yes # GenBank has no D. virilis ESTs at this point... that may change. droVir1.genbank.est.native.load = no droVir1.downloadDir = droVir1 droVir1.perChromTables = no # droVir2 (D. virilis) # genbank has 35 mRNAs and 633 ESTs at time of initial build droVir2.serverGenome = /hive/data/genomes/droVir2/droVir2.2bit droVir2.clusterGenome = /scratch/data/droVir2/droVir2.2bit droVir2.ooc = /scratch/data/droVir2/11.ooc droVir2.lift = no droVir2.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} droVir2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} droVir2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} droVir2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} droVir2.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} droVir2.refseq.mrna.native.load = yes droVir2.refseq.mrna.xeno.load = yes droVir2.genbank.mrna.xeno.load = yes droVir2.genbank.est.native.load = yes droVir2.downloadDir = droVir2 droVir2.perChromTables = no # apiMel1 (A. mellifera) apiMel1.serverGenome = /hive/data/genomes/apiMel1/apiMel1.2bit apiMel1.clusterGenome = /scratch/data/apiMel1/apiMel1.2bit apiMel1.ooc = /scratch/data/apiMel2/11.ooc apiMel1.lift = no apiMel1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} apiMel1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} apiMel1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} apiMel1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} apiMel1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} apiMel1.refseq.mrna.native.load = no apiMel1.genbank.mrna.xeno.load = yes apiMel1.downloadDir = apiMel1 apiMel1.perChromTables = no # apiMel2 (A. mellifera) apiMel2.serverGenome = /hive/data/genomes/apiMel2/nib/*.nib apiMel2.clusterGenome = /scratch/data/apiMel2/nib/*.nib apiMel2.ooc = /scratch/data/apiMel2/11.ooc apiMel2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} apiMel2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} apiMel2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} apiMel2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} apiMel2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} apiMel2.lift = no apiMel2.refseq.mrna.native.load = no apiMel2.genbank.mrna.xeno.load = yes apiMel2.downloadDir = apiMel2 apiMel2.perChromTables = no # droEre1 (D. erecta) droEre1.serverGenome = /hive/data/genomes/droEre1/droEre1.2bit droEre1.clusterGenome = /scratch/data/droEre1/droEre1.2bit droEre1.ooc = /scratch/data/droEre1/11.ooc droEre1.lift = no droEre1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} droEre1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} droEre1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} droEre1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} droEre1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} droEre1.refseq.mrna.native.load = no droEre1.refseq.mrna.xeno.load = yes droEre1.genbank.mrna.xeno.load = yes # GenBank has no D. erecta ESTs at this point... that may change. droEre1.genbank.est.native.load = no droEre1.downloadDir = droEre1 droEre1.perChromTables = no # monDom5 (M. domestica) 8 chroms plus X and Un monDom5.serverGenome = /hive/data/genomes/monDom5/monDom5.2bit monDom5.clusterGenome = /scratch/data/monDom5/monDom5.2bit monDom5.ooc = /scratch/data/monDom5/11.ooc monDom5.lift = /hive/data/genomes/monDom5/jkStuff/liftAll.lft monDom5.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} monDom5.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} monDom5.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} monDom5.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} monDom5.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} monDom5.downloadDir = monDom5 monDom5.refseq.mrna.xeno.load = yes monDom5.refseq.mrna.xeno.loadDesc = yes monDom5.genbank.mrna.xeno.load = yes monDom5.perChromTables = no monDom5.upstreamGeneTbl = refGene monDom5.upstreamMaf = multiz9way /hive/data/genomes/monDom5/bed/multiz9way/species.lst # monDom4 (M. domestica) 8 chroms plus X and Un monDom4.serverGenome = /hive/data/genomes/monDom4/monDom4.2bit monDom4.clusterGenome = /scratch/data/monDom4/monDom4.2bit monDom4.ooc = /scratch/data/monDom4/11.ooc monDom4.lift = no monDom4.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} monDom4.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} monDom4.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} monDom4.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} monDom4.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} monDom4.downloadDir = monDom4 monDom4.refseq.mrna.xeno.load = yes monDom4.refseq.mrna.xeno.loadDesc = yes monDom4.genbank.mrna.xeno.load = yes monDom4.upstreamGeneTbl = ensGene monDom4.upstreamMaf = multiz7way /hive/data/genomes/monDom4/bed/multiz7way/species.lst # monDom1 (M. domestica) 19,348 scaffolds monDom1.serverGenome = /hive/data/genomes/monDom1/monDom1.2bit monDom1.clusterGenome = /scratch/data/monDom1/monDom1.2bit monDom1.ooc = /scratch/data/monDom1/11.ooc monDom1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} monDom1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} monDom1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} monDom1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} monDom1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} monDom1.refseq.mrna.native.load = no monDom1.genbank.mrna.xeno.load = yes monDom1.genbank.est.native.load = no monDom1.downloadDir = monDom1 monDom1.lift = no monDom1.perChromTables = no # there is no suitable gene table here # monDom1.upstreamGeneTbl = ensGene # cb3 (C. briggsae) cb3.serverGenome = /hive/data/genomes/cb3/cb3.2bit cb3.clusterGenome = /scratch/data/cb3/cb3.2bit cb3.ooc = /scratch/data/cb3/11.ooc cb3.lift = /hive/data/genomes/cb3/jkStuff/liftAll.lft cb3.align.unplacedChroms = chrUn,chr*_random cb3.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} cb3.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} cb3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} cb3.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} cb3.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} cb3.refseq.mrna.native.load = no cb3.refseq.mrna.xeno.load = yes cb3.genbank.mrna.xeno.load = yes cb3.downloadDir = cb3 # cb1 (C. briggsae) cb1.serverGenome = /hive/data/genomes/cb1/chrUn.2bit cb1.clusterGenome = /scratch/data/cb1/chrUn.2bit cb1.ooc = /scratch/data/cb1/11.ooc cb1.align.unplacedChroms = chrUn cb1.lift = /hive/data/genomes/cb1/Un/chrUn.lft cb1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} cb1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} cb1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} cb1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} cb1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} cb1.refseq.mrna.native.load = yes cb1.refseq.mrna.xeno.load = yes cb1.genbank.mrna.xeno.load = no cb1.downloadDir = cbJul2002 cb1.perChromTables = no # droSim1 (D. simulans) droSim1.serverGenome = /hive/data/genomes/droSim1/droSim1.2bit droSim1.clusterGenome = /scratch/data/droSim1/droSim1.2bit droSim1.ooc = /scratch/data/droSim1/11.ooc droSim1.lift = /hive/data/genomes/droSim1/jkStuff/liftAll.lft droSim1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} droSim1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} droSim1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} droSim1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} droSim1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} droSim1.refseq.mrna.native.load = no droSim1.refseq.mrna.xeno.load = yes droSim1.genbank.mrna.xeno.load = yes droSim1.downloadDir = droSim1 # droGri1 (D. grimshawi) droGri1.serverGenome = /hive/data/genomes/droGri1/droGri1.2bit droGri1.clusterGenome = /scratch/data/droGri1/droGri1.2bit droGri1.lift = no droGri1.ooc=/scratch/data/droGri1/11.ooc droGri1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} droGri1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} droGri1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} droGri1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} droGri1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} droGri1.refseq.mrna.native.load = no droGri1.refseq.mrna.xeno.load = yes # GenBank has no D. grimshawi mRNAs nor ESTs at this point... that may change. droGri1.genbank.mrna.native.load = no droGri1.genbank.mrna.xeno.load = yes droGri1.genbank.est.native.load = no droGri1.downloadDir = droGri1 droGri1.perChromTables = no # droYak2 (D. yakuba) droYak2.serverGenome = /hive/data/genomes/droYak2/droYak2.2bit droYak2.clusterGenome = /scratch/data/droYak2/droYak2.2bit droYak2.ooc = /scratch/data/droYak2/11.ooc droYak2.lift = /hive/data/genomes/droYak2/jkStuff/liftAll.lft droYak2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} droYak2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} droYak2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} droYak2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} droYak2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} droYak2.refseq.mrna.native.load = no droYak2.refseq.mrna.xeno.load = yes droYak2.genbank.mrna.xeno.load = yes droYak2.downloadDir = droYak2 # droPer1 (D. persimilis) # genbank.150.0/full has 1 mRNA and 0 ESTs at time of initial build, # so no need to make native tracks. droPer1.serverGenome = /hive/data/genomes/droPer1/droPer1.2bit droPer1.clusterGenome = /scratch/data/droPer1/droPer1.2bit droPer1.ooc = /scratch/data/droPer1/11.ooc droPer1.lift = no droPer1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} droPer1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} droPer1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} droPer1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} droPer1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} droPer1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} droPer1.refseq.mrna.native.load = no droPer1.refseq.mrna.xeno.load = yes droPer1.genbank.mrna.native.load = no droPer1.genbank.mrna.xeno.load = yes droPer1.genbank.est.native.load = no droPer1.downloadDir = droPer1 droPer1.perChromTables = no # droSec1 (D. sechellia) # genbank.150.0/full has 7 mRNAs and 0 ESTs at time of initial build, # so no need to make native tracks. droSec1.serverGenome = /hive/data/genomes/droSec1/droSec1.2bit droSec1.clusterGenome = /scratch/data/droSec1/droSec1.2bit droSec1.ooc = /scratch/data/droSec1/11.ooc droSec1.lift = no droSec1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} droSec1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} droSec1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} droSec1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} droSec1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} droSec1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} droSec1.refseq.mrna.native.load = no droSec1.refseq.mrna.xeno.load = yes droSec1.genbank.mrna.native.load = no droSec1.genbank.mrna.xeno.load = yes droSec1.genbank.est.native.load = no droSec1.downloadDir = droSec1 droSec1.perChromTables = no # nemVec1 (Starlet Sea Anemone) # Per Mark: only load if >10^3 available - /hive/data/genomes/genbank/data/organism.lst # organism mrnaCnt estCnt refSeqCnt nemVec1.serverGenome = /hive/data/genomes/nemVec1/nemVec1.2bit nemVec1.clusterGenome = /scratch/data/nemVec1/nemVec1.2bit nemVec1.ooc = /scratch/data/nemVec1/11.ooc nemVec1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} nemVec1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} nemVec1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} nemVec1.maxIntron = 100000 nemVec1.lift = no nemVec1.genbank.est.native.load = yes nemVec1.genbank.est.xeno.load = no nemVec1.genbank.mrna.native.load = no nemVec1.genbank.mrna.xeno.load = yes nemVec1.refseq.mrna.xeno.load = yes nemVec1.refseq.mrna.native.load = no nemVec1.perChromTables = no nemVec1.downloadDir = nemVec1 # aplCal1 - (Sea Hare Broad WGS Aplcal 2.0) # Assembly Accession: AASC00000000.2 aplCal1.serverGenome = /hive/data/genomes/aplCal1/aplCal1.2bit aplCal1.clusterGenome = /scratch/data/aplCal1/aplCal1.2bit aplCal1.ooc = /scratch/data/aplCal1/11.ooc aplCal1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} aplCal1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} aplCal1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} aplCal1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} aplCal1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} aplCal1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} aplCal1.refseq.mrna.native.load = no aplCal1.genbank.est.native.load = yes aplCal1.genbank.est.xeno.load = no aplCal1.refseq.mrna.xeno.load = yes aplCal1.refseq.mrna.xeno.loadDesc = yes aplCal1.perChromTables = no aplCal1.downloadDir = aplCal1 aplCal1.genbank.mrna.blatTargetDb = yes aplCal1.lift = no # # Please keep organisms together and in assending order rather than adding at # the end #