src/hg/makeDb/doc/hg18.txt 1.421

Index: src/hg/makeDb/doc/hg18.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg18.txt,v
retrieving revision 1.420
retrieving revision 1.421
diff -b -B -U 4 -r1.420 -r1.421
--- src/hg/makeDb/doc/hg18.txt	16 May 2010 20:34:30 -0000	1.420
+++ src/hg/makeDb/doc/hg18.txt	1 Jun 2010 17:56:24 -0000	1.421
@@ -30134,4 +30134,39 @@
     # Modern Human Seq:	bamMMS4 bamMMS5 bamMMS6 bamMMS7 bamMMS8
     # Neandertal Mito:	ntMito
 
 #############################################################################
+# BUILD DECIPHER TRACK (DONE, 6/1/10, Fan)
+
+ssh hgwdev
+
+# Received raw DECIPHER data file, daa_28-05-10_ucsc.txt, 
+# from Manuel Corpas [mc10@sanger.ac.uk] and place it under
+# /hive/data/outside/decipher/
+
+cd /hive/data/genomes/gs.19/build36/bed
+mkdir decipher
+cd decipher
+
+cp -p /hive/data/outside/decipher/daa_28-05-10_ucsc.txt .
+
+hgsql hg18 -e 'drop table decipherRaw'
+hgsql hg18 < ~/src/hg/lib/decipherRaw.sql
+
+# load into decipherRaw table
+hgsql hg18 -e \
+'load data local infile "daa_28-05-10_ucsc.txt" into table decipherRaw ignore 1 lines'
+
+# construct the bed file, decipher.bed
+hgsql hg18 -N -e 'select "chr", chr, start-1, end, id from decipherRaw ' |\
+sed -e 's/chr\t/chr/' |sort -u>j.tmp
+# fix some out of range of entries
+cat j.tmp|sed -e 's/243000000/242951149/' |\
+sed -e 's/115090019/114142980/' >decipher.bed
+rm j.tmp
+
+# load the bed track.
+hgLoadBed hg18 decipher decipher.bed
+
+# create knownToDecipher table.
+hgMapToGene -all hg18 decipher knownGene knownToDecipher
+#############################################################################