src/hg/makeDb/doc/therKoda1.txt 1.3
1.3 2009/11/25 21:48:42 hiram
change autoScaleDefault to autoScale
Index: src/hg/makeDb/doc/therKoda1.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/therKoda1.txt,v
retrieving revision 1.2
retrieving revision 1.3
diff -b -B -U 1000000 -r1.2 -r1.3
--- src/hg/makeDb/doc/therKoda1.txt 26 Jul 2006 16:59:59 -0000 1.2
+++ src/hg/makeDb/doc/therKoda1.txt 25 Nov 2009 21:48:42 -0000 1.3
@@ -1,181 +1,181 @@
# 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
- # autoScaleDefault 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/