src/hg/makeDb/doc/mm9.txt 1.96

1.96 2009/06/10 23:12:29 hartera
Re-loaded the miRNA track after adding scores that correspond to whether the sequence is on the + or - strand.

Index: src/hg/makeDb/doc/mm9.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/mm9.txt,v
retrieving revision 1.95
retrieving revision 1.96
diff -b -B -U 4 -r1.95 -r1.96
--- src/hg/makeDb/doc/mm9.txt	10 Jun 2009 19:16:49 -0000	1.95
+++ src/hg/makeDb/doc/mm9.txt	10 Jun 2009 23:12:29 -0000	1.96
@@ -9392,10 +9392,13 @@
     sed -e 's/\";//g' mmMirBaseFormat.gff | sed -e 's/ID=\"//g' \
        | sed -e 's/ACC=\"MI[0-9]*\s//' > mmMirBaseFormatIdOnly.gff
     # chr1    .       miRNA   20669091        20669163        .       +
     # .       mmu-mir-206
+    # use score 906 for + strand and 480 for - strand. This will show 
+    # up black on the track for + strand and grey for - strand.
     awk 'BEGIN {FS="\t"} {OFS="\t"} \
-        {if ($0 !~ /#/) print $1, $4, $5, $9, "0", $7}' \
+        {if ($0 !~ /#/ && $7 == "+") print $1, $4, $5, $9, 960, $7; \
+       else if ($0 !~ /#/ && $7 == "-") print $1, $4, $5, $9, 480, $7;}' \
         mmMirBaseFormatIdOnly.gff > mmMirBaseFormatIdOnly.bed
     # Remove previous table
     hgsql -e 'drop table miRNA' mm9
     hgLoadBed mm9 miRNA mmMirBaseFormatIdOnly.bed