042fb28210e075fdf13711d9f634bddfd7e97e74
hiram
  Tue Mar 2 11:08:14 2021 -0800
liftOver to rn7 refs #26682

diff --git src/hg/makeDb/doc/rn6.txt src/hg/makeDb/doc/rn6.txt
index 7993208..dc58452 100644
--- src/hg/makeDb/doc/rn6.txt
+++ src/hg/makeDb/doc/rn6.txt
@@ -4503,16 +4503,37 @@
             -noDbNameCheck -syntenicNet) > swap.log 2>&1
     #  real    79m18.904s
 
     cat fb.regenCho1.chainRn6Link.txt
     # 1694175880 bases of 2266312740 (74.755%) in intersection
     cat fb.regenCho1.chainSynRn6Link.txt
     # 1402196536 bases of 2266312740 (61.871%) in intersection
 
     time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
 	regenCho1 rn6) > rbest.log 2>&1 &
     # real    1687m33.035s
 
     cat fb.regenCho1.chainRBest.Rn6.txt
     # 1435220608 bases of 2266312740 (63.328%) in intersection
 
-#########################################################################
+##############################################################################
+# LIFTOVER TO rn7 (DONE - 2021-02-04 - Hiram)
+    ssh hgwdev
+    mkdir /hive/data/genomes/rn6/bed/blat.rn7.2021-02-04
+    cd /hive/data/genomes/rn6/bed/blat.rn7.2021-02-04
+    doSameSpeciesLiftOver.pl -verbose=2 \
+        -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
+        -query2Bit=/hive/data/genomes/rn7/rn7.2bit \
+        -querySizes=/hive/data/genomes/rn7/chrom.sizes \
+        -ooc=/hive/data/genomes/rn6/jkStuff/rn6.11.ooc \
+         rn6 rn7
+    time (doSameSpeciesLiftOver.pl -verbose=2 \
+        -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
+        -query2Bit=/hive/data/genomes/rn7/rn7.2bit \
+        -querySizes=/hive/data/genomes/rn7/chrom.sizes \
+        -ooc=/hive/data/genomes/rn6/jkStuff/rn6.11.ooc \
+         rn6 rn7) > doLiftOverToRn7.log 2>&1
+    # real    317m44.103s
+
+    # see if the liftOver menus function in the browser from rn6 to rn7
+
+##############################################################################