4e87889264ce4941bd458eaea3190c95d9b682c5
hiram
  Sun Dec 11 15:23:30 2022 -0800
liftOver to canFam6 per user request refs #30374

diff --git src/hg/makeDb/doc/canFam2.txt src/hg/makeDb/doc/canFam2.txt
index e6daacc..81e7087 100644
--- src/hg/makeDb/doc/canFam2.txt
+++ src/hg/makeDb/doc/canFam2.txt
@@ -3283,16 +3283,43 @@
     cat Tracks_nuclear_NumtS_CAmFAm2 | grep -v "^track" > canFam2NumtS.bed
     cat  Tracks_NumtS_assembled_CanFam2 | grep -v "^track" > canFam2NumtSAssembled.bed
     cat Tracks_mit_NumtS_CanFam2 | grep -v "^track" >  canFam2NumtSMitochondrion.bed
 
     # load the 3 bed files to canFam2
     hgLoadBed canFam2  numtSAssembled  canFam2NumtSAssembled.bed
     hgLoadBed canFam2 numtS canFam2NumtS.bed
     hgLoadBed canFam2 numtSMitochondrion canFam2NumtSMitochondrion.bed
     # Make /gbdb/ links and load bam
     mkdir /gbdb/canFam2/NumtS
     ln -s `pwd`/CanFam-2_NumtS_seqs.sorted.bam{,.bai} /gbdb/canFam2/NumtS/
     hgBbiDbLink canFam2 bamAllNumtSSorted /gbdb/canFam2/NumtS/CanFam-2_NumtS_seqs.sorted.bam
     # setup trackDb for canFam2
 
 
-############################################################################
+##############################################################################
+# LIFTOVER TO canFam6 (DONE - 2022-12-07 - Hiram)
+    ssh hgwdev
+    mkdir /hive/data/genomes/canFam2/bed/blat.canFam6.2022-12-07
+    cd /hive/data/genomes/canFam2/bed/blat.canFam6.2022-12-07
+    doSameSpeciesLiftOver.pl -verbose=2 \
+        -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
+        -target2Bit=/hive/data/genomes/canFam2/canFam2.2bit \
+        -targetSizes=/hive/data/genomes/canFam2/chrom.sizes \
+        -query2Bit=/hive/data/genomes/canFam6/canFam6.2bit \
+        -querySizes=/hive/data/genomes/canFam6/chrom.sizes \
+        -ooc=/hive/data/genomes/canFam2/11.ooc \
+         canFam2 canFam6
+    time (doSameSpeciesLiftOver.pl -verbose=2 \
+        -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
+        -target2Bit=/hive/data/genomes/canFam2/canFam2.2bit \
+        -targetSizes=/hive/data/genomes/canFam2/chrom.sizes \
+        -query2Bit=/hive/data/genomes/canFam6/canFam6.2bit \
+        -querySizes=/hive/data/genomes/canFam6/chrom.sizes \
+        -ooc=/hive/data/genomes/canFam2/11.ooc \
+         canFam2 canFam6) > doLiftOverToCanFam6.log 2>&1
+    # this was a difficult alignment, must be some unmasked repeats
+    # in canFam2
+    # real    4625m38.987s
+
+    # see if the liftOver menus function in the browser from canFam2 to canFam6
+
+##############################################################################