src/hg/makeDb/doc/hg18.txt 1.420

Index: src/hg/makeDb/doc/hg18.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg18.txt,v
retrieving revision 1.419
retrieving revision 1.420
diff -b -B -U 4 -r1.419 -r1.420
--- src/hg/makeDb/doc/hg18.txt	14 May 2010 20:47:06 -0000	1.419
+++ src/hg/makeDb/doc/hg18.txt	16 May 2010 20:34:30 -0000	1.420
@@ -29323,8 +29323,10 @@
 # appropriate to have a Signal track as for the ENCODE RNA-seq data tracks. 
 # 2010-02-09, hartera. Create bedGraph Signal subtracks for each tissue/cell
 # using reads/per million mapped reads as the data value.
 # 2010-02-17, hartera. Updated trackDb.ra entry to include views.
+# 2010-05-15 and 2010-05-16, hartera. Re-created the Signal subtracks using 
+# the -bed12 option of bedItemOverlapCount so that blocks are used.
 
    mkdir /hive/groups/gencode/browser/hg18/burgeRnaSeqGemMapperAlign
    cd /hive/groups/gencode/browser/hg18/burgeRnaSeqGemMapperAlign
 
@@ -29420,22 +29422,30 @@
    end
    # Changed track type in trackDb/human/trackDb.ra to bed 12 and 
    # then did make alpha in trackDb directory.
 
-   # 2010-02-09. Add a Signal track so it is easier to view the data in 
-   # regions where there is a high density of reads. 
+   # 2010-02-17
+   # trackDb.ra entry in trackDb/human was updated to include views for the
+   # Raw Signal and Alignment subtracks.
+
+   # 2010-05-15 and 2010-05-16. Add Signal tracks so it is easier to view the 
+   # data in regions where there is a high density of reads. 
    cd /hive/data/genomes/hg18/bed/burgeRnaSeqGemMapperAlign
    # Use bedItemOverlapCount to get counts of overlapping items for each base.
    # Need to sort the bed files and then get the number of reads mapped for
    # that tissue. Divide the counts by the number of million mapped reads to
    # get reads per million mapped reads as the data value. 
+   # Re-make the subtracks using the -bed12 option so that blocks are used 
+   # instead of just the first three fields of the BED file as is the default.
+   rm *.count *.bedGraph
    foreach f (`ls *.bed`)
       echo $f
       set g=$f:r
-      sort $f | bedItemOverlapCount hg18 stdin > ${f}.count
+      sort ${f} | bedItemOverlapCount -bed12 hg18 stdin > ${f}.count
       set size=`hgsql -Ne "select count(distinct name) from ${g};" hg18`
       awk -v size=${size} 'BEGIN {OFS="\t"} {print $1,$2,$3,($4 / (size/1000000));}' ${f}.count > ${g}.bedGraph
    end
+
    # Load the bedGraph tables into the database as Raw Signal tracks.
    foreach f (`ls *.bedGraph`)
       echo $f
       set g=$f:r 
@@ -29438,13 +29448,11 @@
    # Load the bedGraph tables into the database as Raw Signal tracks.
    foreach f (`ls *.bedGraph`)
       echo $f
       set g=$f:r 
+      hgsql -e "drop table ${g}AllRawSignal;" hg18
       hgLoadBed -bedGraph=4 hg18 ${g}AllRawSignal $f >>& load.log
    end
-   # 2010-02-17
-   # trackDb.ra entry in trackDb/human was updated to include views for the
-   # Raw Signal and Alignment subtracks.
 
 ############################################################################
 # TRANSMAP vertebrate.2009-09-13 build  (2009-09-20 markd)