src/hg/makeDb/doc/otoGar1.txt 1.9
1.9 2009/07/21 21:01:45 markd
added transmap update blurb
Index: src/hg/makeDb/doc/otoGar1.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/otoGar1.txt,v
retrieving revision 1.8
retrieving revision 1.9
diff -b -B -U 1000000 -r1.8 -r1.9
--- src/hg/makeDb/doc/otoGar1.txt 21 Oct 2008 20:35:06 -0000 1.8
+++ src/hg/makeDb/doc/otoGar1.txt 21 Jul 2009 21:01:45 -0000 1.9
@@ -1,140 +1,149 @@
#This is the first release of the low-coverage 1.5X assembly of the bushbaby
#(Otolemur garnettii). The genome sequencing and assembly is provided by the
#Broad Institute.
#
#The N50 size is the length such that 50% of the assembled genome lies in
#blocks of the N50 size or longer. The N50 length for supercontigs is 101.35 kb
#and is 3.13 kb for contigs. The total number of bases in supercontigs is 3.39
#Gb and in contigs is 1.97 Gb.
#
##########################################################################
# Run the makeGenomeDb.pl script (DONE - 2006-12-18 - Robert)
# prepare for the makeGenomeDb.pl script:
ssh hgwdev
cd /cluster/data/otoGar1
cat << '_EOF_' > otoGar1.config.ra
# Config parameters for makeGenomeDb.pl:
db otoGar1
clade vertebrate
genomeCladePriority 16
commonName Bushbaby
scientificName Otolemur garnetti
assemblyDate Dec. 2006
assemblyLabel Broad version 1
orderKey 16
fakeAgpMinContigGap 25
fakeAgpMinScaffoldGap 25
mitoAcc none
fastaFiles /cluster/data/otoGar1/fromBroad/Draft_v1.agp.chromosome.fasta
dbDbSpeciesDir bushbaby
_EOF_
~/kent/src/hg/utils/automation/makeGenomeDb.pl otoGar1.config.ra
~/kent/src/hg/utils/automation/makeGenomeDb.pl otoGar1.config.ra -continue agp
#########################################################################
#WindowMasker
ssh kolossus
cd /cluster/data/otoGar1/bed
~/kent/src/hg/utils/automation/doWindowMasker.pl otoGar1 -workhorse=kolossus > wmRun.log 2>&1 &
ssh hgwdev
cd /cluster/data/otoGar1/bed/WindowMasker.2006-12-18/
hgLoadBed otoGar1 windowmasker windowmasker.bed.gz
#########################################################################
# SIMPLE REPEATS (TRF) (DONE 2006-12-19 - Robert)
ssh kolossus
mkdir /cluster/data/otoGar1/bed/simpleRepeat
cd /cluster/data/otoGar1/bed/simpleRepeat
nice -n 19 time twoBitToFa ../../otoGar1.unmasked.2bit stdout \
| trfBig -trf=/cluster/bin/i386/trf stdin /dev/null \
-bedAt=simpleRepeat.bed -tempDir=/tmp > trf.log 2>&1 &
# Make a filtered version for sequence masking:
awk '{if ($5 <= 12) print;}' simpleRepeat.bed > trfMask.bed
splitFileByColumn trfMask.bed trfMaskChrom
# Load unfiltered repeats into the database:
ssh hgwdev
hgLoadBed otoGar1 simpleRepeat \
/cluster/data/otoGar1/bed/simpleRepeat/simpleRepeat.bed \
-sqlTable=$HOME/kent/src/hg/lib/simpleRepeat.sql
featureBits otoGar1 simpleRepeat
#########################################################################
# Mask seeds with orrb to do better alignments - Robert
download and compile orrb from www.drive5.com/orrb and copy to
/cluster/bin/i386/orrb
mkdir /cluster/data/otoGar1/orrb
cd /cluster/data/otoGar1/orrb
twoBitToFa ../otoGar1/otoGar1.unmasked.2bit \
/san/sanvol1/scratch/otoGar/otoGar1.fa
/cluster/bin/i386/orrb -mask /san/sanvol1/scratch/otoGar/otoGar1.fa \
-target /san/sanvol1/scratch/otoGar/otoGar1.fa\
-out otoGar1.maskOrrb.fa -wordsize 11 -threshalpha 13 \
-pattern 00011111000
#########################################################################
## Processing photograph (DONE - 2007-02-15 - Hiram)
ssh hgwdev
mkdir /cluster/data/otoGar1/photograph
cd /cluster/data/otoGar1/photograph
cp -p /usr/local/apache/htdocs/images/Bu* ./BushBaby.jpg
convert -quality 80 -normalize -sharpen 0 -geometry 200x320 BushBaby.jpg \
Otolemur_garnettii.jpg
# add Otolemur_garnettii.jpg to the browser doc source tree and copy
# to /usr/local/apache/htdocs/images
# It is still a bit dark, a -gamma argument could lighten it
################################################
# DOWNLOADS (2007-06-05 kate)
ssh kkstore05
cd /cluster/data/otoGar1
mkdir bigZips
cd bigZips
nice twoBitToFa ../otoGar1.2bit otoGar1.fa
nice gzip otoGar1.fa
md5sum *.gz > md5sum.txt
ssh hgwdev
set d = /usr/local/apache/htdocs/goldenPath
set bd = /cluster/data/otoGar1
cp $d/sorAra1/bigZips/README.txt $bd/bigZips
# EDIT
mkdir -p $d/otoGar1/bigZips
ln -s $bd/bigZips/{*.gz,md5sum.txt,README.txt} $d/otoGar1/bigZips
############################################################################
## BLASTZ swap from mm9 alignments (2007-11-11 - markd)
ssh hgwdev
mkdir /cluster/data/otoGar1/bed/blastz.mm9.swap
cd /cluster/data/otoGar1/bed/blastz.mm9.swap
ln -s blastz.mm9.swap ../blastz.mm9
/cluster/bin/scripts/doBlastzChainNet.pl \
-swap /cluster/data/mm9/bed/blastz.otoGar1/DEF >& swap.out&
# fb.otoGar1.chainMm9Link.txt:
# 592429209 bases of 1969052059 (30.087%) in intersection
############################################################################
# TRANSMAP vertebrate.2008-05-20 build (2008-05-24 markd)
vertebrate-wide transMap alignments were built Tracks are created and loaded
by a single Makefile. This is available from:
svn+ssh://hgwdev.cse.ucsc.edu/projects/compbio/usr/markd/svn/projs/transMap/tags/vertebrate.2008-05-20
see doc/builds.txt for specific details.
############################################################################
############################################################################
# TRANSMAP vertebrate.2008-06-07 build (2008-06-30 markd)
vertebrate-wide transMap alignments were built Tracks are created and loaded
by a single Makefile. This is available from:
svn+ssh://hgwdev.cse.ucsc.edu/projects/compbio/usr/markd/svn/projs/transMap/tags/vertebrate.2008-06-30
see doc/builds.txt for specific details.
############################################################################
# add NCBI identifiers to the dbDb (DONE - 2008-10-21 - Hiram)
hgsql -e 'update dbDb set
sourceName="Broad version 1 (NCBI project 16955, AAQR00000000)" where name="otoGar1";' hgcentraltest
###########################################################################
+############################################################################
+# TRANSMAP vertebrate.2009-07-01 build (2009-07-21 markd)
+
+vertebrate-wide transMap alignments were built Tracks are created and loaded
+by a single Makefile. This is available from:
+ svn+ssh://hgwdev.cse.ucsc.edu/projects/compbio/usr/markd/svn/projs/transMap/tags/vertebrate.2009-07-01
+
+see doc/builds.txt for specific details.
+############################################################################