Index: src/hg/makeDb/doc/mm9.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/mm9.txt,v
retrieving revision 1.116
retrieving revision 1.117
diff -b -B -U 4 -r1.116 -r1.117
--- src/hg/makeDb/doc/mm9.txt	6 Nov 2009 22:38:30 -0000	1.116
+++ src/hg/makeDb/doc/mm9.txt	19 Dec 2009 00:57:58 -0000	1.117
@@ -9854,4 +9854,25 @@
     'load data local infile "GN_mouse_RefSeq.txt" into table geneNetworkId'
 
 #########################################################################
 
+# LASTZ/CHAIN/NET swap danRer6 (DONE - 2009-12-18 - Galt)
+    # original alignment to danRer6
+    cd /hive/data/genomes/danRer6/bed/lastzMm9.2009-12-17
+    cat fb.danRer6.chainMm9Link.txt 
+    #   77099032 bases of 1506896106 (5.116%) in intersection
+
+    #	running the swap - DONE - 2009-12-18
+    mkdir /hive/data/genomes/mm9/bed/blastz.danRer6.swap
+    cd /hive/data/genomes/mm9/bed/blastz.danRer6.swap
+    time nice +19 doBlastzChainNet.pl -verbose=2 \
+        /hive/data/genomes/danRer6/bed/lastzMm9.2009-12-17/DEF \
+	-noLoadChainSplit -chainMinScore=5000 -chainLinearGap=loose \
+	-workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
+	-swap >& swap.log &
+    #	real    183m21.102s
+# TODO BOOKMARK
+    cat fb.mm9.chainDanRer6Link.txt 
+    #	96424507 bases of 1506896106 (6.399%) in intersection
+
+
+#######################################################################

