src/hg/makeDb/doc/hg19.txt 1.40

Index: src/hg/makeDb/doc/hg19.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg19.txt,v
retrieving revision 1.39
retrieving revision 1.40
diff -b -B -U 4 -r1.39 -r1.40
--- src/hg/makeDb/doc/hg19.txt	24 Sep 2009 20:57:52 -0000	1.39
+++ src/hg/makeDb/doc/hg19.txt	30 Sep 2009 19:30:56 -0000	1.40
@@ -6252,5 +6252,35 @@
 by a single Makefile. This is available from:
    svn+ssh://hgwdev.cse.ucsc.edu/projects/compbio/usr/markd/svn/projs/transMap/tags/vertebrate.2009-09-13
 
 see doc/builds.txt for specific details.
-############################################################################
+
+##########################################################################
+# BUILD ALLEN BRAIN TRACK (DONE 09/30/09 kent)
+
+# Make the working directory
+    ssh hgwdev
+    cd /cluster/data/hg19/bed
+    mkdir allenBrain
+    cd allenBrain
+
+# Remap the probe alignments from mm7 to hg18
+
+    zcat /gbdb/mm9/liftOver/mm9ToHg19.over.chain.gz \
+        |  pslMap -chainMapFile -swapMap \
+	       /cluster/data/mm9/bed/allenBrain/allenBrainAli.psl stdin stdout \
+	  |  sort -k 14,14 -k 16,16n > unscored.psl
+
+    pslRecalcMatch unscored.psl /cluster/data/hg19/hg19.2bit \
+        /cluster/data/mm9/bed/allenBrain/allenBrainProbes.fa allenBrainAli.psl
+
+# Load the database
+   hgsql hg19 < ~/kent/src/hg/lib/allenBrainUrl.sql
+   hgsql hg19 -e 'load data local infile "/cluster/data/mm9/bed/allenBrain/allenBrainUrl.tab" into table allenBrainUrl;'
+   hgLoadPsl hg19 allenBrainAli.psl
+   mkdir /gbdb/hg19/allenBrain
+   ln -s /cluster/data/mm9/bed/allenBrain/allenBrainProbes.fa /gbdb/hg19/allenBrain/allenBrainProbes.fa
+   hgLoadSeq hg19 /gbdb/hg19/allenBrain/allenBrainProbes.fa
+
+# Make mapping between known genes and allenBrain
+   hgMapToGene hg19 allenBrainAli -type=psl knownGene knownToAllenBrain
+