# for emacs: -*- mode: sh; -*- # This file describes building the browser database for the archaeal # species Thermococcus kodakaraensis # # if this is the first time you are making your own hgwdev browser, need to do # cd ~/kent/src/, then a make # DOWNLOAD SEQUENCE FROM GENBANK (DONE 10/05) mkdir /cluster/store5/archae/therKoda1 ln -s /cluster/store5/archae/therKoda1 /cluster/data/therKoda1 cd /cluster/data/therKoda1 cp /projects/lowelab/db/Bacteria/Thermococcus_kodakaraensis_KOD1/Ther_koda_KOD1* . mv Ther_koda_KOD1.fa therKoda1.fa grep ">" therKoda1.fa # Edit header of therKoda1.fa seqs to '>chr >plasmid_pNRC100 >plasmid_pNRC200' faToTwoBit therKoda1.fa therKoda1.2bit mkdir /gbdb/therKoda1 ln -s /cluster/data/therKoda1/therKoda1.2bit /gbdb/therKoda1/therKoda1.2bit # CREATE DATABASES AND A BUNCH OF INITIAL STUFF (DONE 10/05) ssh hgwdev echo 'create database therKoda1' | hgsql '' cd /cluster/data/therKoda1 faSize -detailed therKoda1.fa > chrom.sizes echo "create table grp (PRIMARY KEY(NAME)) select * from hg16.grp" | hgsql therKoda1 echo 'INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk) values ("therKoda1", "May 2004", "/gbdb/therKoda1", "Thermococcus kodakaraensis", "chr:500000-550000", 1, 270, "Thermococcus kodakaraensis","Thermococcus kodakaraensis KOD1", "/gbdb/therKoda1/html/description.html", 0);' | hgsql hgcentraltest echo 'INSERT INTO defaultDb (genome, name) values ("Thermococcus kodakaraensis", "therKoda1");' | hgsql hgcentraltest echo 'INSERT INTO genomeClade (genome, clade, priority) values ("Thermococcus kodakaraensis", "archaea",85);' | hgsql hgcentraltest # CREATE CHROMINFO TABLE (DONE 10/05) ssh hgwdev cd /cluster/data/therKoda1 cp ~baertsch/kent/src/hg/lib/chromInfo.sql . hgsql therKoda1 < chromInfo.sql echo "load data local infile 'chrom.sizes' into table chromInfo" | hgsql therKoda1 echo "update chromInfo set fileName = '/gbdb/therKoda1/therKoda1.2bit'" | hgsql therKoda1 cd ~/kent/src/hg/makeDb/trackDb # add the trackDb directories mkdir -p archae/therKoda1 cvs add archae/therKoda1 cvs commit archae/therKoda1 make DBS=therKoda1 # GC20BASE (DONE 10/05) mkdir -p /cluster/data/therKoda1/bed/gc20Base cd /cluster/data/therKoda1/bed/gc20Base hgGcPercent -wigOut -doGaps -file=stdout -overlap=10 -win=20 therKoda1 /cluster/data/therKoda1/ | wigEncode stdin gc20Base.wig gc20Base.wib cd /cluster/data/therKoda1/bed/gc20Base mkdir /gbdb/therKoda1/wib ln -s `pwd`/gc20Base.wib /gbdb/therKoda1/wib hgLoadWiggle -pathPrefix=/gbdb/therKoda1/wib therKoda1 gc20Base gc20Base.wig # verify index is correct: hgsql therKoda1 -e "show index from gc20Base;" # should see good numbers in Cardinality column # TANDEM REPEAT MASKER (DONE 10/05) ssh hgwdev mkdir -p /cluster/data/therKoda1/bed/simpleRepeat cd /cluster/data/therKoda1 trfBig therKoda1.fa /dev/null -bedAt=/cluster/data/therKoda1/bed/simpleRepeat/chr.bed cd /cluster/data/therKoda1/bed/simpleRepeat hgLoadBed therKoda1 simpleRepeat *.bed -sqlTable=/cluster/home/lowe/kent/src/hg/lib/simpleRepeat.sql # MULTIZ with P. abyssi, P. hori, P. furi # DONE (10/9/05), kpollard mkdir -p /cluster/data/therKoda1/bed/conservation cd /cluster/data/therKoda1/bed/conservation cp /cluster/data/pyrFur2/bed/conservation/HoxD55.q . cp /cluster/data/pyrFur2/bed/conservation/*.chr . cp /cluster/data/pyrFur2/bed/conservation/*.nib . faSize -detailed *.chr > chrom.sizes #blastz blastz therKoda1.chr pyrFur2.chr Q=HoxD55.q > therKoda1-pyrFur2.lav blastz therKoda1.chr pyrAby1.chr Q=HoxD55.q > therKoda1-pyrAby1.lav blastz therKoda1.chr pyrHor1.chr Q=HoxD55.q > therKoda1-pyrHor1.lav #lavToAxt /cluster/bin/i386/lavToAxt therKoda1-pyrFur2.lav . . therKoda1-pyrFur2.axt /cluster/bin/i386/lavToAxt therKoda1-pyrAby1.lav . . therKoda1-pyrAby1.axt /cluster/bin/i386/lavToAxt therKoda1-pyrHor1.lav . . therKoda1-pyrHor1.axt #axtBest axtBest therKoda1-pyrFur2.axt therKoda1.chr -winSize=500 -minScore=5000 therKoda1-pyrFur2-best.axt axtBest therKoda1-pyrAby1.axt therKoda1.chr -winSize=500 -minScore=5000 therKoda1-pyrAby1-best.axt axtBest therKoda1-pyrHor1.axt therKoda1.chr -winSize=500 -minScore=5000 therKoda1-pyrHor1-best.axt #axtToMaf axtToMaf therKoda1-pyrFur2-best.axt chrom.sizes chrom.sizes therKoda1-pyrFur2.maf axtToMaf therKoda1-pyrAby1-best.axt chrom.sizes chrom.sizes therKoda1-pyrAby1.maf axtToMaf therKoda1-pyrHor1-best.axt chrom.sizes chrom.sizes therKoda1-pyrHor1.maf #multiz #delete extra header lines from maf files multiz therKoda1-pyrAby1.maf therKoda1-pyrHor1.maf - > therKoda1-pyrAby1-pyrHor1.maf multiz therKoda1-pyrFur2.maf therKoda1-pyrAby1-pyrHor1.maf - > therKoda1-pyrAby1-pyrHor1-pyrFur2.maf #phyloHMM /cluster/bin/phast/msa_view -i MAF -M therKoda1.chr -o SS therKoda1-pyrAby1-pyrHor1-pyrFur2.maf > therKoda1.ss /cluster/bin/phast/phyloFit -i SS therKoda1.ss -t "((pyrFur2,(pyrHor1,pyrAby1)),therKoda1)" /cluster/bin/phast/msa_view -i SS therKoda1.ss --summary-only /cluster/bin/phast/phastCons therKoda1.ss phyloFit.mod --gc 0.4611 \ --target-coverage 0.7 --estimate-trees pyr-tree \ --expected-lengths 25 --no-post-probs --ignore-missing \ --nrates 1,1 /cluster/bin/phast/phastCons therKoda1.ss \ pyr-tree.cons.mod,pyr-tree.noncons.mod \ --target-coverage 0.7 --expected-lengths 25 \ --viterbi therKoda1-elements.bed --score \ --require-informative 0 --seqname chr > cons.dat wigEncode cons.dat phastCons.wig phastCons.wib draw_tree phyloFit.mod > pyr-tree.ps #check similar to pyrFur2 tree #move data mkdir wib mv phastCons.wib wib/phastCons.wib mv phastCons.wig wib/phastCons.wig ln -s /cluster/data/therKoda1/bed/conservation/wib/phastCons.wib /gbdb/therKoda1/wib mkdir -p /gbdb/therKoda1/pwMaf mkdir -p otherSpp/pyrFur2 otherSpp/pyrAby1 otherSpp/pyrHor1 mv therKoda1-pyrFur2.maf otherSpp/pyrFur2/chr.maf mv therKoda1-pyrAby1.maf otherSpp/pyrAby1/chr.maf mv therKoda1-pyrHor1.maf otherSpp/pyrHor1/chr.maf ln -s /cluster/data/therKoda1/bed/conservation/otherSpp/pyrFur2 /gbdb/therKoda1/pwMaf/pyrFur2_pwMaf ln -s /cluster/data/therKoda1/bed/conservation/otherSpp/pyrAby1 /gbdb/therKoda1/pwMaf/pyrAby1_pwMaf ln -s /cluster/data/therKoda1/bed/conservation/otherSpp/pyrHor1 /gbdb/therKoda1/pwMaf/pyrHor1_pwMaf mkdir multiz mv therKoda1-pyrAby1-pyrHor1-pyrFur2.maf multiz/chr.maf ln -s /cluster/data/therKoda1/bed/conservation/multiz /gbdb/therKoda1/multizTk1Pa1Ph1Pf2 #load hgLoadWiggle therKoda1 phastCons /cluster/data/therKoda1/bed/conservation/wib/phastCons.wig hgLoadMaf -warn therKoda1 multizTk1Pa1Ph1Pf2 hgLoadMaf -warn therKoda1 pyrFur2_pwMaf -pathPrefix=/gbdb/therKoda1/pwMaf/pyrFur2_pwMaf hgLoadMaf -warn therKoda1 pyrAby1_pwMaf -pathPrefix=/gbdb/therKoda1/pwMaf/pyrAby1_pwMaf hgLoadMaf -warn therKoda1 pyrHor1_pwMaf -pathPrefix=/gbdb/therKoda1/pwMaf/pyrHor1_pwMaf hgLoadBed therKoda1 phastConsElements therKoda1-elements.bed #trackDb cd ~/kent/src/hg/makeDb/trackDb/archae/ mkdir therKoda1 cvs add therKoda1 cd therKoda1 #trackDb.ra entry # track multizTk1Pa1Ph1Pf2 # shortLabel Conservation # longLabel Pyrococcus 4-way multiz alignments # group compGeno # priority 10.0 # visibility pack # type wigMaf 0.0 1.0 # maxHeightPixels 100:40:11 # wiggle phastCons # yLineOnOff Off # autoScale Off # pairwise pwMaf # speciesOrder pyrAby1 pyrHor1 pyrFur2 cvs add trackDb.ra cvs commit -m "New multiz track" trackDb.ra #html page for multizTk1Pa1Ph1Pf2 cvs add multizTk1Pa1Ph1Pf2.html cvs commit -m "Details page for multiz track" multizTk1Pa1Ph1Pf2.html # DESCRIPTION PAGE (DONE 10/20/05), kpollard # Write ~/kent/src/hg/makeDb/trackDb/archae/therKoda1/description.html cd ~/kent/src/hg/makeDb/trackDb/archae/therKoda1/ chmod a+r description.html cvs add description.html cvs commit -m "description page" description.html mkdir -p /cluster/data/therKoda1/html/ cp ~/kent/src/hg/makeDb/trackDb/archae/therKoda1/description.html \ /cluster/data/therKoda1/html/description.html mkdir -p /gbdb/therKoda1/html ln -s /cluster/data/therKoda1/html/description.html /gbdb/therKoda1/html/