src/hg/makeDb/doc/pyrAby1.txt 1.3

Index: src/hg/makeDb/doc/pyrAby1.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/pyrAby1.txt,v
retrieving revision 1.2
retrieving revision 1.3
diff -b -B -U 1000000 -r1.2 -r1.3
--- src/hg/makeDb/doc/pyrAby1.txt	23 Jan 2008 21:49:37 -0000	1.2
+++ src/hg/makeDb/doc/pyrAby1.txt	25 Nov 2009 21:48:42 -0000	1.3
@@ -1,91 +1,91 @@
 #No documentation of basic browser up til now...
 
 # MULTIZ with P. furi, P. hori, T. kodakarensis
 # This is redo of an earlier run, so some files are already in place
 # DONE (10/8/05), kpollard
 
     mkdir -p /cluster/data/pyrAby1/bed/conservation
     cd /cluster/data/pyrAby1/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 pyrAby1.chr pyrFur2.chr Q=HoxD55.q > pyrAby1-pyrFur2.lav
     blastz pyrAby1.chr pyrHor1.chr Q=HoxD55.q > pyrAby1-pyrHor1.lav
     blastz pyrAby1.chr therKoda1.chr Q=HoxD55.q > pyrAby1-therKoda1.lav
     #lavToAxt
     /cluster/bin/i386/lavToAxt pyrAby1-pyrFur2.lav . . pyrAby1-pyrFur2.axt
     /cluster/bin/i386/lavToAxt pyrAby1-pyrHor1.lav . . pyrAby1-pyrHor1.axt
     /cluster/bin/i386/lavToAxt pyrAby1-therKoda1.lav . . pyrAby1-therKoda1.axt
     #axtBest
     axtBest pyrAby1-pyrFur2.axt pyrAby1.chr -winSize=500 -minScore=5000 pyrAby1-pyrFur2-best.axt
     axtBest pyrAby1-pyrHor1.axt pyrAby1.chr -winSize=500 -minScore=5000 pyrAby1-pyrHor1-best.axt
     axtBest pyrAby1-therKoda1.axt pyrAby1.chr -winSize=500 -minScore=5000 pyrAby1-therKoda1-best.axt
     #axtToMaf
     axtToMaf pyrAby1-pyrFur2-best.axt chrom.sizes chrom.sizes pyrAby1-pyrFur2.maf
      axtToMaf pyrAby1-pyrHor1-best.axt chrom.sizes chrom.sizes pyrAby1-pyrHor1.maf
      axtToMaf pyrAby1-therKoda1-best.axt chrom.sizes chrom.sizes pyrAby1-therKoda1.maf
     #multiz
     #delete extra header lines from maf files
     multiz pyrAby1-pyrHor1.maf pyrAby1-pyrFur2.maf - > pyrAby1-pyrHor1-pyrFur2.maf
     multiz pyrAby1-therKoda1.maf pyrAby1-pyrHor1-pyrFur2.maf - > pyrAby1-pyrHor1-pyrFur2-therKoda1.maf
     #phyloHMM
     /cluster/bin/phast/msa_view -i MAF -M pyrAby1.chr -o SS pyrAby1-pyrHor1-pyrFur2-therKoda1.maf > pyrAby1.ss
     /cluster/bin/phast/phyloFit -i SS pyrAby1.ss -t "((pyrFur2,(pyrAby1,pyrHor1)),therKoda1)" 
     /cluster/bin/phast/msa_view -i SS pyrAby1.ss --summary-only
     /cluster/bin/phast/phastCons pyrAby1.ss phyloFit.mod --gc 0.4522 \
 	--target-coverage 0.7 --estimate-trees pyr-tree \
 	--expected-lengths 25 --no-post-probs --ignore-missing \
 	--nrates 1,1
     /cluster/bin/phast/phastCons pyrAby1.ss \
 	pyr-tree.cons.mod,pyr-tree.noncons.mod \
 	--target-coverage 0.7 --expected-lengths 25 \
 	--viterbi pyrAby1-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/pyrAby1/bed/conservation/wib/phastCons.wib /gbdb/pyrAby1/wib
     mkdir -p /gbdb/pyrAby1/pwMaf
     mkdir -p otherSpp/pyrFur2 otherSpp/pyrHor1 otherSpp/therKoda1
     mv pyrAby1-pyrFur2.maf otherSpp/pyrFur2/chr.maf
     mv pyrAby1-pyrHor1.maf otherSpp/pyrHor1/chr.maf
     mv pyrAby1-therKoda1.maf otherSpp/therKoda1/chr.maf
     ln -s /cluster/data/pyrAby1/bed/conservation/otherSpp/pyrFur2 /gbdb/pyrAby1/pwMaf/pyrFur2_pwMaf
     ln -s /cluster/data/pyrAby1/bed/conservation/otherSpp/pyrHor1 /gbdb/pyrAby1/pwMaf/pyrHor1_pwMaf
     ln -s /cluster/data/pyrAby1/bed/conservation/otherSpp/therKoda1 /gbdb/pyrAby1/pwMaf/therKoda1_pwMaf
     mkdir multiz
     mv pyrAby1-pyrHor1-pyrFur2-therKoda1.maf multiz/chr.maf
     ln -s /cluster/data/pyrAby1/bed/conservation/multiz /gbdb/pyrAby1/multizPa1Ph1Pf2Tk1
     #load
     hgLoadWiggle pyrAby1 phastCons /cluster/data/pyrAby1/bed/conservation/wib/phastCons.wig
     hgLoadMaf -warn pyrAby1 multizPa1Ph1Pf2Tk1
     hgLoadMaf -warn pyrAby1 pyrFur2_pwMaf -pathPrefix=/gbdb/pyrAby1/pwMaf/pyrFur2_pwMaf
     hgLoadMaf -warn pyrAby1 pyrHor1_pwMaf -pathPrefix=/gbdb/pyrAby1/pwMaf/pyrHor1_pwMaf
     hgLoadMaf -warn pyrAby1 therKoda1_pwMaf -pathPrefix=/gbdb/pyrAby1/pwMaf/therKoda1_pwMaf
     hgLoadBed pyrAby1 phastConsElements pyrAby1-elements.bed 
     #trackDb
     cd ~/kent/src/hg/makeDb/trackDb/archae/pyrAby1
     #trackDb.ra entry
     # track multizPa1Ph1Pf2Tk1
     # 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 pyrHor1 pyrFur2 therKoda1
     cvs commit -m "New multiz track" trackDb.ra
     #html page for multizPa1Ph1Pf2Tk1
     cvs add multizPa1Ph1Pf2Tk1.html
     cvs commit -m "Details page for multiz track" multizPa1Ph1Pf2Tk1.html