src/hg/makeDb/doc/hg19.txt 1.74
1.74 2010/01/25 19:16:13 hiram
panda aligned to dog,rat,mouse,human,opossum pig aligned to mouse,human,opossum,cow bosTau4 to rn4, rabbit to rat,mouse,opossum,guineaPig
Index: src/hg/makeDb/doc/hg19.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg19.txt,v
retrieving revision 1.73
retrieving revision 1.74
diff -b -B -U 4 -r1.73 -r1.74
--- src/hg/makeDb/doc/hg19.txt 25 Jan 2010 16:46:58 -0000 1.73
+++ src/hg/makeDb/doc/hg19.txt 25 Jan 2010 19:16:13 -0000 1.74
@@ -8328,8 +8328,112 @@
-tab -sqlTable=$HOME/kent/src/hg/lib/gwasCatalog.sql -notItemRgb -allowStartEqualEnd
########################################################################
+# ailMel1 Panda alignment (DONE - 2010-01-21 - Hiram)
+ mkdir /hive/data/genomes/hg19/bed/lastzAilMel1.2010-01-21
+ cd /hive/data/genomes/hg19/bed/lastzAilMel1.2010-01-21
+
+ cat << '_EOF_' > DEF
+# Human vs. Panda
+# parameters from the Panda paper supplemental where they describe
+# their lastz parameters
+BLASTZ_K=2200
+BLASTZ_Y=3400
+BLASTZ_L=6000
+BLASTZ_H=2000
+BLASTZ_C=2
+BLASTZ_T=2
+
+# our usual M
+BLASTZ_M=50
+
+# TARGET: Human Hg19
+SEQ1_DIR=/scratch/data/hg19/nib
+SEQ1_LEN=/scratch/data/hg19/chrom.sizes
+SEQ1_CHUNK=10000000
+SEQ1_LAP=10000
+
+# QUERY: Panda
+SEQ2_DIR=/scratch/data/ailMel1/ailMel1.2bit
+SEQ2_LEN=/scratch/data/ailMel1/chrom.sizes
+SEQ2_CHUNK=10000000
+SEQ2_LIMIT=50
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/hg19/bed/lastzAilMel1.2010-01-21
+TMPDIR=/scratch/tmp
+'_EOF_'
+ # << happy emacs
+
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ `pwd`/DEF \
+ -noLoadChainSplit -syntenicNet \
+ -workhorse=hgwdev -smallClusterHub=pk -bigClusterHub=swarm \
+ -chainMinScore=3000 -chainLinearGap=medium > do.log 2>&1 &
+ # real 150m41.538s
+ cat fb.hg19.chainAilMel1Link.txt
+ # 1449290504 bases of 2897316137 (50.022%) in intersection
+
+ mkdir /hive/data/genomes/ailMel1/bed/blastz.hg19.swap
+ cd /hive/data/genomes/ailMel1/bed/blastz.hg19.swap
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ /hive/data/genomes/hg19/bed/lastzAilMel1.2010-01-21/DEF \
+ -swap -noLoadChainSplit -syntenicNet \
+ -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
+ -chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
+ # real 104m38.416s
+ cat fb.ailMel1.chainHg19Link.txt
+ # 1403163838 bases of 2225124764 (63.060%) in intersection
+
+#########################################################################
+# susScr1 Pig BLASTZ/CHAIN/NET (DONE - 2010-01-21 - Hiram)
+ screen # use a screen to manage this multi-day job
+ mkdir /hive/data/genomes/hg19/bed/lastzSusScr1.2010-01-21
+ cd /hive/data/genomes/hg19/bed/lastzSusScr1.2010-01-21
+
+ cat << '_EOF_' > DEF
+# Pig vs. Human
+BLASTZ_M=50
+
+# TARGET: Human Hg19
+SEQ1_DIR=/scratch/data/hg19/nib
+SEQ1_LEN=/scratch/data/hg19/chrom.sizes
+SEQ1_CHUNK=10000000
+SEQ1_LAP=10000
+
+# QUERY: Pig SusScr1
+SEQ2_DIR=/scratch/data/susScr1/susScr1.2bit
+SEQ2_LEN=/scratch/data/susScr1/chrom.sizes
+SEQ2_CHUNK=10000000
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/hg19/bed/lastzSusScr1.2010-01-21
+TMPDIR=/scratch/tmp
+'_EOF_'
+ # << this line keeps emacs coloring happy
+
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ `pwd`/DEF \
+ -noLoadChainSplit -syntenicNet \
+ -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=pk \
+ -chainMinScore=3000 -chainLinearGap=medium > do.log 2>&1 &
+ # real 1072m48.949s
+ cat fb.hg19.chainSusScr1Link.txt
+ # 1198793067 bases of 2897316137 (41.376%) in intersection
+
+ mkdir /hive/data/genomes/susScr1/bed/blastz.hg19.swap
+ cd /hive/data/genomes/susScr1/bed/blastz.hg19.swap
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ /hive/data/genomes/hg19/bed/lastzSusScr1.2010-01-21/DEF \
+ -swap -noLoadChainSplit -syntenicNet \
+ -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=pk \
+ -chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
+ # real 119m14.040s
+ cat fb.susScr1.chainHg19Link.txt
+ # 1272787231 bases of 2231332019 (57.042%) in intersection
+
+#########################################################################
# PERSONAL GENOME VARIANTS (DONE 12/29/09 giardine)
# liftOver track files in /hive/data/genomes/hg18/bed/pgSnp/