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

diff --git src/hg/makeDb/doc/mm9.txt src/hg/makeDb/doc/mm9.txt
index f4f1ca9..d33cfe9 100644
--- src/hg/makeDb/doc/mm9.txt
+++ src/hg/makeDb/doc/mm9.txt
@@ -12630,15 +12630,43 @@
 
     cat  fb.galGal4.chainMm9Link.txt
     #	84283201 bases of 1032854810 (8.160%) in intersection
 
     time (doRecipBest.pl -buildDir=`pwd` galGal4 mm9) > rbest.log 2>&1
     # continuing after hive difficulties and finish recipBest step manually
     time (doRecipBest.pl -workhorse=hgwdev -continue=download  -buildDir=`pwd` \
       galGal4 mm9) > download.log 2>&1
     # real    0m4.386s
 
 #########################################################################
 # Crispr track. See ../crisprTrack/README.txt (2016-12-15 max)
 # Command: doCrispr.sh mm9 ensGene
 ##############################################################################
 
+##############################################################################
+# LIFTOVER TO mm39 (DONE - 2022-10-24 - Hiram)
+    ssh hgwdev
+    mkdir /hive/data/genomes/mm9/bed/blat.mm39.2022-10-24
+    cd /hive/data/genomes/mm9/bed/blat.mm39.2022-10-24
+    doSameSpeciesLiftOver.pl -verbose=2 \
+        -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
+        -target2Bit=/hive/data/genomes/mm9/mm9.2bit \
+        -targetSizes=/hive/data/genomes/mm9/chrom.sizes \
+        -query2Bit=/hive/data/genomes/mm39/mm39.2bit \
+        -querySizes=/hive/data/genomes/mm39/chrom.sizes \
+        -ooc=/hive/data/genomes/mm9/11.ooc \
+         mm9 mm39
+    time (doSameSpeciesLiftOver.pl -verbose=2 \
+        -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
+        -target2Bit=/hive/data/genomes/mm9/mm9.2bit \
+        -targetSizes=/hive/data/genomes/mm9/chrom.sizes \
+        -query2Bit=/hive/data/genomes/mm39/mm39.2bit \
+        -querySizes=/hive/data/genomes/mm39/chrom.sizes \
+        -ooc=/hive/data/genomes/mm9/11.ooc \
+         mm9 mm39) > doLiftOverToMm39.log 2>&1
+    # performed in two steps
+    # real    212m47.631s
+    # real    128m9.574s
+
+    # see if the liftOver menus function in the browser from mm9 to mm39
+
+##############################################################################