src/hg/makeDb/doc/galGal3.txt 1.28
1.28 2009/07/02 22:21:43 hiram
Rerun all the equCab2 chains and nets to clean up problems
Index: src/hg/makeDb/doc/galGal3.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/galGal3.txt,v
retrieving revision 1.27
retrieving revision 1.28
diff -b -B -U 4 -r1.27 -r1.28
--- src/hg/makeDb/doc/galGal3.txt 13 Mar 2009 23:55:40 -0000 1.27
+++ src/hg/makeDb/doc/galGal3.txt 2 Jul 2009 22:21:43 -0000 1.28
@@ -2673,4 +2673,55 @@
searchType genePred
termRegex chr[0-9a-zA-Z_]+\.([0-9]+|pasa)\.[0-9]+(\.[0-9a-z]+)?
searchPriority 50
+############################################################################
+# Re-Run equCab2 alignment (DONE - 2009-06-29,07-01 - Hiram)
+ mkdir /hive/data/genomes/galGal3/bed/lastzEquCab2.2009-06-29
+ cd /hive/data/genomes/galGal3/bed/lastzEquCab2.2009-06-29
+
+ cat << '_EOF_' > DEF
+# Chicken vs. Horse
+
+BLASTZ_M=50
+
+# TARGET: Human galGal3
+SEQ1_DIR=/scratch/data/galGal3/bothMaskedNibs
+SEQ1_LEN=/scratch/data/galGal3/chrom.sizes
+SEQ1_CHUNK=10000000
+SEQ1_LAP=10000
+
+# QUERY: Horse
+SEQ2_DIR=/scratch/data/equCab2/equCab2.2bit
+SEQ2_LEN=/scratch/data/equCab2/chrom.sizes
+SEQ2_CTGDIR=/hive/data/genomes/equCab2/equCab2.UnScaffolds.2bit
+SEQ2_CTGLEN=/hive/data/genomes/equCab2/equCab2.UnScaffolds.sizes
+SEQ2_LIFT=/hive/data/genomes/equCab2/jkStuff/equCab2.chrUn.lift
+SEQ2_CHUNK=20000000
+SEQ2_LIMIT=100
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/galGal3/bed/lastzEquCab2.2009-06-29
+TMPDIR=/scratch/tmp
+'_EOF_'
+ # << happy emacs
+
+ time doBlastzChainNet.pl `pwd`/DEF \
+ -noLoadChainSplit -verbose=2 -bigClusterHub=pk \
+ -workhorse=hgwdev \
+ -chainMinScore=3000 -chainLinearGap=medium > do.log 2>&1 &
+ # real 220m54.623s
+ # cat fb.galGal3.chainEquCab2Link.txt
+ # 68476046 bases of 1042591351 (6.568%) in intersection
+
+ mkdir /hive/data/genomes/equCab2/bed/blastz.galGal3.swap
+ cd /hive/data/genomes/equCab2/bed/blastz.galGal3.swap
+ time doBlastzChainNet.pl \
+ /hive/data/genomes/galGal3/bed/lastzEquCab2.2009-06-29/DEF \
+ -noLoadChainSplit -verbose=2 -bigClusterHub=pk \
+ -swap -workhorse=hgwdev \
+ -chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
+ # real 10m1.381s
+ cat fb.equCab2.chainGalGal3Link.txt
+ # 73336799 bases of 2428790173 (3.019%) in intersection
+
+############################################################################