5cd914bd3782a8a0a26ac2e8d7af9d13db79b2f8
hiram
  Wed Oct 26 12:10:56 2022 -0700
mm9 vs mm39 liftOvers in both directions

diff --git src/hg/makeDb/doc/mm39/initialBuild.txt src/hg/makeDb/doc/mm39/initialBuild.txt
index efcdda1..3f8a734 100644
--- src/hg/makeDb/doc/mm39/initialBuild.txt
+++ src/hg/makeDb/doc/mm39/initialBuild.txt
@@ -1420,16 +1420,41 @@
     #  22
 
     printf '# UCSC to Ensembl chr name translation
 CREATE TABLE ucscToEnsembl (
     ucsc varchar(255) not null,        # UCSC chromosome name
     ensembl varchar(255) not null,     # Ensembl chromosome name
               #Indices
     PRIMARY KEY(ucsc(22))
 );
 ' > ucscToEnsembl.sql
 
     hgLoadSqlTab mm39 ucscToEnsembl ucscToEnsembl.sql ucscToEnsembl.tab
 
     # verify the blue bar "ensembl" link is now available under the 'View'
     # tab
-#############################################################################
+##############################################################################
+# LIFTOVER TO mm9 (DONE - 2022-10-25 - Hiram)
+    ssh hgwdev
+    mkdir /hive/data/genomes/mm39/bed/blat.mm9.2022-10-25
+    cd /hive/data/genomes/mm39/bed/blat.mm9.2022-10-25
+    doSameSpeciesLiftOver.pl -verbose=2 \
+        -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
+        -query2Bit=/hive/data/genomes/mm39/mm39.2bit \
+        -querySizes=/hive/data/genomes/mm39/chrom.sizes \
+        -target2Bit=/hive/data/genomes/mm9/mm9.2bit \
+        -targetSizes=/hive/data/genomes/mm9/chrom.sizes \
+        -ooc=/hive/data/genomes/mm39/jkStuff/mm39.11.ooc \
+         mm39 mm9
+    time (doSameSpeciesLiftOver.pl -verbose=2 \
+        -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
+        -query2Bit=/hive/data/genomes/mm39/mm39.2bit \
+        -querySizes=/hive/data/genomes/mm39/chrom.sizes \
+        -target2Bit=/hive/data/genomes/mm9/mm9.2bit \
+        -targetSizes=/hive/data/genomes/mm9/chrom.sizes \
+        -ooc=/hive/data/genomes/mm39/jkStuff/mm39.11.ooc \
+         mm39 mm9) > doLiftOverToMm9.log 2>&1
+    # real    246m16.388s
+
+    # see if the liftOver menus function in the browser from mm39 to mm9
+
+##############################################################################