src/hg/makeDb/doc/hg16.txt 1.12

1.12 2010/04/02 17:25:19 angie
Regenerated kgTargetAli from knownGene table (instead of wrong build dir), but didn't reload -- Ann and I feel it's not worth the QA effort. 
Index: src/hg/makeDb/doc/hg16.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg16.txt,v
retrieving revision 1.11
retrieving revision 1.12
diff -b -B -U 4 -r1.11 -r1.12
--- src/hg/makeDb/doc/hg16.txt	25 Nov 2009 21:48:39 -0000	1.11
+++ src/hg/makeDb/doc/hg16.txt	2 Apr 2010 17:25:19 -0000	1.12
@@ -11892,42 +11892,45 @@
 hg16.upstreamMaf = mzPt1Mm3Rn3Gg2_pHMM /hive/data/genomes/hg16/bed/multiz.hg16mm3rn3panTro1galGal2/species.lst
 
 
 #############################################################################
-# MAKE PCR TARGET FOR UCSC GENES (DONE 11/4/08 angie)
+# MAKE PCR TARGET FOR UCSC GENES (REGENERATED BUT NOT RELOADED 4/2/10 angie)
+# Originally done 11/4/08 (with file from not quite the right UCSC Genes build directory,
+# resulting in some missing genes in kgTargetAli)
     ssh hgwdev
     mkdir /cluster/data/hg16/bed/mrnaPcr
     cd /cluster/data/hg16/bed/mrnaPcr
     # First, get consistent FA and PSL for UCSC Genes.
-    genePredToBed /cluster/data/hg16/bed/kgHg16C/kgBestMrna/knownGene.tab \
+    hgsql hg16 -NBe 'select * from knownGene' | cut -f 1-10 > knownGene.gp
+    genePredToBed knownGene.gp \
       > ucscGenes.bed
     hgsql hg16 -NBe 'select kgId,geneSymbol from kgXref' \
     | perl -wpe 's/^(\S+)\t(\S+)/$1\t${1}__$2/ || die;' \
       > idSub.txt
     subColumn 4 ucscGenes.bed idSub.txt ucscGenesIdSubbed.bed
     sequenceForBed -keepName -db=hg16 -bedIn=ucscGenesIdSubbed.bed \
       -fastaOut=stdout \
     | faToTwoBit -ignoreDups stdin kgTargetSeq.2bit
-    cut -f 1-10 /cluster/data/hg16/bed/kgHg16C/kgBestMrna/knownGene.tab \
+    cut -f 1-10 knownGene.gp \
     | genePredToFakePsl hg16 stdin kgTargetAli.psl /dev/null
 
+# NOT DONE -- not worth QA effort:
     # Load up the UCSC Genes target PSL table and put 2bit in /gbdb::
-    cd /cluster/data/hg16/bed/mrnaPcr
-    hgLoadPsl hg16 kgTargetAli.psl
+    hgLoadPsl hg16 -table=kgTargetAliMar10 kgTargetAli.psl
     mkdir /gbdb/hg16/targetDb
-    ln -s /cluster/data/hg16/bed/mrnaPcr/kgTargetSeq.2bit /gbdb/hg16/targetDb/
+    ln -s /cluster/data/hg16/bed/mrnaPcr/kgTargetSeq.2bit /gbdb/hg16/targetDb/kgTargetSeqMar10.2bit
 
     # Ask cluster-admin to start an untranslated, -stepSize=5 gfServer on
     # /gbdb/hg16/targetDb/kgTargetSeq.2bit .
 
     ssh hgwdev
     # Add records to hgcentraltest blatServers and targetDb:
     hgsql hgcentraltest -e \
-      'INSERT into blatServers values ("hg16Kg", "blat13", 17795, 0, 1);'
+      'INSERT into blatServers values ("hg16KgMar10", "blat13", 17795, 0, 1);'
     hgsql hgcentraltest -e \
-      'INSERT into targetDb values("hg16Kg", "UCSC Genes", \
-         "hg16", "kgTargetAli", "", "", \
-         "/gbdb/hg16/targetDb/kgTargetSeq.2bit", 1, now(), "");'
+      'INSERT into targetDb values("hg16KgMar10", "UCSC Genes", \
+         "hg16", "kgTargetAliMar10", "", "", \
+         "/gbdb/hg16/targetDb/kgTargetSeqMar10.2bit", 1, now(), "");'
 
 
 #############################################################################
 # LIFTOVER TO Hg19 (DONE - 2009-04-24 - Hiram )