src/hg/makeDb/doc/danRer6.txt 1.15
1.15 2009/12/23 19:02:44 galt
danRer6 xentro2 chains
Index: src/hg/makeDb/doc/danRer6.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/danRer6.txt,v
retrieving revision 1.14
retrieving revision 1.15
diff -b -B -U 4 -r1.14 -r1.15
--- src/hg/makeDb/doc/danRer6.txt 23 Dec 2009 05:47:20 -0000 1.14
+++ src/hg/makeDb/doc/danRer6.txt 23 Dec 2009 19:02:44 -0000 1.15
@@ -933,9 +933,9 @@
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
+# zebrafish vs. stickleback
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
@@ -970,8 +970,51 @@
cat fb.danRer6.chainGasAcu1Link.txt
# 147479454 bases of 1506896106 (9.787%) in intersection
+#########################################################################
+# LASTZ Xenopus xenTro2 (DONE - 2009-12-22 - Galt)
+ mkdir /hive/data/genomes/danRer6/bed/lastzXenTro2.2009-12-22
+ cd /hive/data/genomes/danRer6/bed/lastzXenTro2.2009-12-22
+
+ cat << '_EOF_' > DEF
+# zebrafish vs. xenopus
+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: Xenopus xenTro2
+SEQ2_DIR=/scratch/data/xenTro2/xenTro2.2bit
+SEQ2_LEN=/scratch/data/xenTro2/chrom.sizes
+SEQ2_CHUNK=10000000
+SEQ2_LAP=10000
+SEQ2_LIMIT=50
+
+BASE=/hive/data/genomes/danRer6/bed/lastzXenTro2.2009-12-22
+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.chainXenTro2Link.txt
+ # 100078259 bases of 1506896106 (6.641%) in intersection
+
############################################################################
# TRANSMAP vertebrate.2009-09-13 build (2009-09-20 markd)
vertebrate-wide transMap alignments were built Tracks are created and loaded