Index: src/hg/makeDb/doc/hg18.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg18.txt,v
retrieving revision 1.391
retrieving revision 1.392
diff -b -B -U 4 -r1.391 -r1.392
--- src/hg/makeDb/doc/hg18.txt	12 Dec 2009 04:39:22 -0000	1.391
+++ src/hg/makeDb/doc/hg18.txt	15 Dec 2009 18:48:11 -0000	1.392
@@ -28896,8 +28896,11 @@
 #############################################################################
 # BURGE	LAB DATA MAPPED WITH GEMMAPPER. PROVIDED BY THOMAS DERRIEN FROM RODERIC
 # GUIGO'S LAB AT CRG. (E-MAIL: thomas.derrien@crg.es)
 # (hartera, 2009-09-13 - 2009-09-16, DONE) 
+# 2009-12-14. Set cdsStart = cdsEnd = 0. Moved track data directory to 
+# /hive/data/genomes/hg18/bed.
+
    mkdir /hive/groups/gencode/browser/hg18/burgeRnaSeqGemMapperAlign
    cd /hive/groups/gencode/browser/hg18/burgeRnaSeqGemMapperAlign
 
    wget --timestamping "http://genome.imim.es/~tderrien/Gencode/For_Rachel/GFF_Burge_32bp_Gencode2b/GSM325476_brain_HCT168_hg18.fa.GEM_index.hg18.gencode_data.rel2b.length_32.gff.gz"
@@ -28955,8 +28958,21 @@
      > load.log &
    # Added a trackDb entry in 
    # ccds/trunk/gencode/browser/trackDb/human/hg18/trackDb.ra
 
+   # 2009-12-14, Need to change cdsStart = cdsEnd = 0 in the table as this
+   # data should have no CDS defined. Currently cdsStart = cdsEnd = txEnd. 
+   cd /hive/groups/gencode/browser/hg18/burgeRnaSeqGemMapperAlign
+   hgsql -Ne 'show tables like "burge%";' hg18 > burgeTables
+   foreach t (`cat burgeTables`)
+      echo $t
+      hgsql -e "update $t set cdsStart = 0;" hg18
+      hgsql -e "update $t set cdsEnd = 0;" hg18
+   end
+   # Then move data to directory in hg18 genome bed directory
+   cd /hive/data/genomes/hg18/bed
+   mv /hive/groups/gencode/browser/hg18/burgeRnaSeqGemMapperAlign ./
+  
 ############################################################################
 # TRANSMAP vertebrate.2009-09-13 build  (2009-09-20 markd)
 
 vertebrate-wide transMap alignments were built  Tracks are created and loaded

