src/hg/makeDb/doc/metMar1.txt 1.3

Index: src/hg/makeDb/doc/metMar1.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/metMar1.txt,v
retrieving revision 1.2
retrieving revision 1.3
diff -b -B -U 1000000 -r1.2 -r1.3
--- src/hg/makeDb/doc/metMar1.txt	23 Jan 2008 21:49:37 -0000	1.2
+++ src/hg/makeDb/doc/metMar1.txt	25 Nov 2009 21:48:40 -0000	1.3
@@ -1,107 +1,107 @@
 # can't find earlier documentation
 
 # MULTIZ with methKand1, methJann1, methTher1 
 # DONE (10/11/05), kpollard
 
     cd /cluster/data/metMar1/bed/conservation
     cp metJan1.chr methJann1.chr
     cp metThe1.chr methTher1.chr
     cp /cluster/data/methJann1/bed/conservation/methKand1.chr .
     #fix names to be methTher1, methKand1 manually
     sed s/metJan/methJann/ methJann1.chr > temp
     mv temp methJann1.chr
     faToNib metMar1.chr metMar1.chr.nib
     faToNib methTher1.chr methTher1.chr.nib
     faToNib methKand1.chr methKand1.chr.nib
     faToTwoBit methJann1.chr methJann1.2bit
 
     #chrom sizes
     faSize -detailed metMar1.chr methKand1.chr methTher1.chr methJann1.chr > chrom.sizes
 
     #blastz 
     blastz metMar1.chr methJann1.chr Q=HoxD55.q > metMar1-methJann1.lav
     blastz metMar1.chr methTher1.chr Q=HoxD55.q > metMar1-methTher1.lav
     blastz metMar1.chr methKand1.chr Q=HoxD55.q > metMar1-methKand1.lav
 
     /cluster/bin/i386/lavToAxt metMar1-methJann1.lav . methJann1.2bit metMar1-methJann1.axt
     /cluster/bin/i386/lavToAxt metMar1-methTher1.lav . . metMar1-methTher1.axt
     /cluster/bin/i386/lavToAxt metMar1-methKand1.lav . . metMar1-methKand1.axt
 
     axtBest metMar1-methJann1.axt metMar1.chr -winSize=500 -minScore=5000 metMar1-methJann1-best.axt
     axtBest metMar1-methTher1.axt metMar1.chr -winSize=500 -minScore=5000 metMar1-methTher1-best.axt
     axtBest metMar1-methKand1.axt metMar1.chr -winSize=500 -minScore=5000 metMar1-methKand1-best.axt
 
     axtToMaf metMar1-methJann1-best.axt chrom.sizes chrom.sizes metMar1-methJann1.maf
     axtToMaf metMar1-methTher1-best.axt chrom.sizes chrom.sizes metMar1-methTher1.maf
     axtToMaf metMar1-methKand1-best.axt chrom.sizes chrom.sizes metMar1-methKand1.maf
 
     #multiz
     #remove extra header lines
     multiz metMar1-methJann1.maf metMar1-methTher1.maf - > metMar1-methJann1-methTher1.maf
     multiz metMar1-methKand1.maf metMar1-methJann1-methTher1.maf - > metMar1-methJann1-methTher1-methKand1.maf
 
     #phyloHMM
     /cluster/bin/phast/msa_view -i MAF -M metMar1.chr -o SS metMar1-methJann1-methTher1-methKand1.maf > metMar1.ss
     /cluster/bin/phast/phyloFit -i SS metMar1.ss -t "(methKand1,(methTher1,(methJann1,metMar1)))" -o MmMjMtMk
     /cluster/bin/phast/msa_view -i SS metMar1.ss --summary-only
     #add GC content to next call
     /cluster/bin/phast/phastCons metMar1.ss MmMjMtMk.mod --gc 0.3854 \
     --target-coverage 0.7 --estimate-trees met-tree \
     --expected-lengths 25 --no-post-probs --ignore-missing \
     --nrates 1,1
     /cluster/bin/phast/phastCons metMar1.ss \
     met-tree.cons.mod,met-tree.noncons.mod \
     --target-coverage 0.7 --expected-lengths 25 \
     --viterbi metMar1-elements.bed --score \
     --require-informative 0 --seqname chr > cons.dat
     wigEncode cons.dat phastCons.wig phastCons.wib
     /cluster/bin/phast/draw_tree MmMjMtMk.mod > met-tree.ps 
     #make ai and jpg files in Illustrator
     cp met-tree.jpg /usr/local/apache/htdocs/images/metMar1-tree.jpg
 
     #move data
     mkdir wib
     mv phastCons.wib wib/phastCons.wib
     mv phastCons.wig wib/phastCons.wig
     ln -s /cluster/data/metMar1/bed/conservation/wib/phastCons.wib /gbdb/metMar1/wib
     mkdir /gbdb/metMar1/pwMaf
     mkdir -p otherSpp/methJann1 otherSpp/methTher1 otherSpp/methKand1
     mv metMar1-methTher1.maf otherSpp/methTher1/chr.maf
     mv metMar1-methJann1.maf otherSpp/methJann1/chr.maf
     mv metMar1-methKand1.maf otherSpp/methKand1/chr.maf
     ln -s /cluster/data/metMar1/bed/conservation/otherSpp/methTher1 /gbdb/metMar1/pwMaf/methTher1_pwMaf
     ln -s /cluster/data/metMar1/bed/conservation/otherSpp/methKand1 /gbdb/metMar1/pwMaf/methKand1_pwMaf
     ln -s /cluster/data/metMar1/bed/conservation/otherSpp/methJann1 /gbdb/metMar1/pwMaf/methJann1_pwMaf
     mkdir multiz
     mv metMar1-methJann1-methTher1-methKand1.maf multiz/chr.maf
     ln -s /cluster/data/metMar1/bed/conservation/multiz /gbdb/metMar1/multizMmMjMtMk
 
     #load
     hgLoadWiggle metMar1 phastCons /cluster/data/metMar1/bed/conservation/wib/phastCons.wig
     hgLoadMaf -warn metMar1 multizMmMjMtMk
     hgLoadMaf -warn metMar1 methTher1_pwMaf -pathPrefix=/gbdb/metMar1/pwMaf/methTher1_pwMaf
     hgLoadMaf -warn metMar1 methKand1_pwMaf -pathPrefix=/gbdb/metMar1/pwMaf/methKand1_pwMaf
     hgLoadMaf -warn metMar1 methJann1_pwMaf -pathPrefix=/gbdb/metMar1/pwMaf/methJann1_pwMaf
     hgLoadBed metMar1 phastConsElements metMar1-elements.bed 
 
     #trackDb
     cd ~/kent/src/hg/makeDb/trackDb/archae/metMar1
     #trackDb.ra entry
     # track multizMmMjMtMk
     # shortLabel Conservation
     # longLabel Thermoplasma/Ferroplasma/Picrophilus 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 methJann1 methTher1 methKand1
     cvs add trackDb.ra
     cvs commit -m "New multiz track" trackDb.ra
     #html page
     cvs add multizMmMjMtMk.html
     cvs commit -m "Details page for multiz track" multizMmMjMtMk.html