src/hg/makeDb/doc/hg18.txt 1.393

Index: src/hg/makeDb/doc/hg18.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg18.txt,v
retrieving revision 1.392
retrieving revision 1.393
diff -b -B -U 4 -r1.392 -r1.393
--- src/hg/makeDb/doc/hg18.txt	15 Dec 2009 18:48:11 -0000	1.392
+++ src/hg/makeDb/doc/hg18.txt	5 Jan 2010 01:14:06 -0000	1.393
@@ -28896,10 +28896,12 @@
 #############################################################################
 # 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 
+# 2009-12-14, hartera. Set cdsStart = cdsEnd = 0. Moved track data directory to 
 # /hive/data/genomes/hg18/bed.
+# 2010-01-04, hartera. Change the data to BED format and re-loaded tables. BED
+# is more appropriate for this data type.
 
    mkdir /hive/groups/gencode/browser/hg18/burgeRnaSeqGemMapperAlign
    cd /hive/groups/gencode/browser/hg18/burgeRnaSeqGemMapperAlign
 
@@ -28971,8 +28973,31 @@
    # Then move data to directory in hg18 genome bed directory
    cd /hive/data/genomes/hg18/bed
    mv /hive/groups/gencode/browser/hg18/burgeRnaSeqGemMapperAlign ./
   
+   # 2010-01-04 Change the data to BED format. For genePred format, 
+   # there is always a track configuration added for colouring tracks by
+   # genomic codons which does not make sense for this data. Also, BED is
+   # more appropriate for this data type.
+   cd /hive/data/genomes/hg18/bed/burgeRnaSeqGemMapperAlign
+   # Convert gff to genePred and then genePred to BED, drop old table and
+   # then load database with BED format data. Need to fix the cdStart and
+   # cdsEnd fields to be 0. 
+   foreach f (`ls burgeRnaSeqGemMapperAlign*.gff`)
+     echo $f >> bed.log
+     set g=$f:r
+     echo $g
+     ldHgGene -exon=read -nobin -out=${g}.gp hg18 $g $f >>& bed.log
+     awk 'BEGIN {FS="\t"} {OFS="\t"} {print $1,$2,$3,$4,$5,0,0,$8,$9,$10}' \
+         ${g}.gp > ${g}Fixed.gp 
+     genePredToBed ${g}Fixed.gp > ${g}.bed 
+     echo "Dropping table $g"
+     hgsql -e "drop table ${g};" hg18 
+     hgLoadBed hg18 $g ${g}.bed >>& bed.log 
+   end
+   # Changed track type in trackDb/human/trackDb.ra to bed 12 and 
+   # then did make alpha in trackDb directory.
+ 
 ############################################################################
 # TRANSMAP vertebrate.2009-09-13 build  (2009-09-20 markd)
 
 vertebrate-wide transMap alignments were built  Tracks are created and loaded