src/hg/makeDb/doc/hg18.txt 1.392
1.392 2009/12/15 18:48:11 hartera
Changed cdsStart and cdsEnd to be 0 in Burge RNA-seq data and moved track data to directory for hg18 genome assembly.
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