#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. # http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AAQR00 # ########################################################################## # 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. ############################################################################ ############################################################################ # TRANSMAP vertebrate.2009-09-13 build (2009-09-20 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.2009-09-13 see doc/builds.txt for specific details. ############################################################################