src/hg/makeDb/doc/danRer6.txt 1.13

Index: src/hg/makeDb/doc/danRer6.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/danRer6.txt,v
retrieving revision 1.12
retrieving revision 1.13
diff -b -B -U 4 -r1.12 -r1.13
--- src/hg/makeDb/doc/danRer6.txt	19 Dec 2009 00:57:58 -0000	1.12
+++ src/hg/makeDb/doc/danRer6.txt	22 Dec 2009 19:56:42 -0000	1.13
@@ -885,9 +885,9 @@
 
 
 
 #########################################################################
-# LASTZ Zebrafish DanRer6 (DONE - 2009-12-17 - Galt)
+# LASTZ Mouse mm9 (DONE - 2009-12-17 - Galt)
     mkdir /hive/data/genomes/danRer6/bed/lastzMm9.2009-12-17
     cd /hive/data/genomes/danRer6/bed/lastzMm9.2009-12-17
 
     cat << '_EOF_' > DEF
@@ -927,4 +927,47 @@
 
     cat fb.danRer6.chainMm9Link.txt 
     #   77099032 bases of 1506896106 (5.116%) in intersection
 
+#########################################################################
+# LASTZ Stickleback gasAcu1 (DONE - 2009-12-21 - Galt)
+    mkdir /hive/data/genomes/danRer6/bed/lastzGasAcu1.2009-12-21
+    cd /hive/data/genomes/danRer6/bed/lastzGasAcu1.2009-12-21
+
+    cat << '_EOF_' > DEF
+# zebrafish vs. mouse
+BLASTZ_H=2000
+BLASTZ_Y=3400
+BLASTZ_L=6000
+BLASTZ_K=2200
+BLASTZ_Q=/scratch/data/blastz/HoxD55.q
+
+# TARGET: Zebrafish danRer6
+SEQ1_DIR=/scratch/data/danRer6/danRer6.2bit
+SEQ1_LEN=/scratch/data/danRer6/chrom.sizes
+SEQ1_CHUNK=20000000
+SEQ1_LAP=0
+SEQ1_LIMIT=40
+
+# QUERY: Stickleback gasAcu1
+SEQ2_DIR=/scratch/data/gasAcu1/gasAcu1.2bit
+SEQ2_LEN=/scratch/data/gasAcu1/chrom.sizes
+SEQ2_CHUNK=10000000
+SEQ2_LAP=10000
+SEQ2_LIMIT=50
+
+BASE=/hive/data/genomes/danRer6/bed/lastzGasAcu1.2009-12-21
+TMPDIR=/scratch/tmp
+'_EOF_'
+    # << happy emacs
+
+    #	establish a screen to control this job
+    screen
+    time nice +19 doBlastzChainNet.pl -verbose=2 \
+	`pwd`/DEF \
+	-noLoadChainSplit -chainMinScore=5000 -chainLinearGap=loose \
+	-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
+	>& do.log &
+
+    cat fb.danRer6.chainGasAcu1Link.txt 
+    #   147479454 bases of 1506896106 (9.787%) in intersection
+