src/hg/makeDb/doc/mm9.txt 1.98

Index: src/hg/makeDb/doc/mm9.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/mm9.txt,v
retrieving revision 1.97
retrieving revision 1.98
diff -b -B -U 4 -r1.97 -r1.98
--- src/hg/makeDb/doc/mm9.txt	11 Jun 2009 00:11:49 -0000	1.97
+++ src/hg/makeDb/doc/mm9.txt	11 Jun 2009 22:28:31 -0000	1.98
@@ -9363,9 +9363,9 @@
     cat fb.mm9.chainHg19Link.txt 
     #	1013880568 bases of 2620346127 (38.693%) in intersection
 
 #############################################################################
-#  RE-BUILD miRNA TRACK (DONE, 2009-06-09-2009-06-10, hartera)
+#  RE-BUILD miRNA TRACK (DONE, 2009-06-09-2009-06-11, hartera)
     # The miRNA track from miRBase is out of date so update the track. 
     mkdir -p /hive/data/genomes/mm9/bed/miRNA-2009-06-09
     cd /hive/data/genomes/mm9/bed/miRNA-2009-06-09
     # Download GFF file of latest miRNA annotations from miRBase at the
@@ -9393,11 +9393,13 @@
     # 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.
+    # Re-do below and re-load track as appears off by 1 compared to 
+    # Ensembl track and other miRNA resources (2009-06-11)
     awk 'BEGIN {FS="\t"} {OFS="\t"} \
-        {if ($0 !~ /#/ && $7 == "+") print $1, $4, $5, $9, 960, $7; \
-       else if ($0 !~ /#/ && $7 == "-") print $1, $4, $5, $9, 480, $7;}' \
+        {if ($0 !~ /#/ && $7 == "+") print $1, $4-1, $5, $9, 960, $7; \
+       else if ($0 !~ /#/ && $7 == "-") print $1, $4-1, $5, $9, 480, $7;}' \
         mmMirBaseFormatIdOnly.gff > mmMirBaseFormatIdOnly.bed
     # Remove previous table
     hgsql -e 'drop table miRNA' mm9
     hgLoadBed mm9 miRNA mmMirBaseFormatIdOnly.bed