src/hg/makeDb/doc/tetNig2.txt 1.3
1.3 2009/08/06 22:59:01 hiram
Set blat server and default position
Index: src/hg/makeDb/doc/tetNig2.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/tetNig2.txt,v
retrieving revision 1.2
retrieving revision 1.3
diff -b -B -U 1000000 -r1.2 -r1.3
--- src/hg/makeDb/doc/tetNig2.txt 6 Aug 2009 20:57:39 -0000 1.2
+++ src/hg/makeDb/doc/tetNig2.txt 6 Aug 2009 22:59:01 -0000 1.3
@@ -1,192 +1,213 @@
# for emacs: -*- mode: sh; -*-
# Tetraodon Nigirividis from Genoscope, version v8 (released Mar 2007)
# Project website:
# http://www.genoscope.cns.fr/externe/Download/Projets/Projet_C/genomique/goldenpath_v2/
##########################################################################
# Download sequence (DONE - 2009-08-06 - Hiram)
mkdir /hive/data/genomes/tetNig2
cd /hive/data/genomes/tetNig2
mkdir genoscope
cd genoscope
D="http://www.genoscope.cns.fr/externe/Download/Projets/Projet_C/genomique/golde
npath_v2/"
for F in chr.agp chr.agp.info
do
wget --timestamping "${D}/${F}"
done
for C in 1 1_random 2 2_random 3 4 5 6 7 8 9 10 11 12 13 14 15 \
15_random 16 17 18 19 20 21 21_random Un_random
do
wget --timestamping "${D}/unmasked/chr${C}.fa.bz2"
done
for F in Tetraodon_mRNAs_v8.2.fa Tetraodon_peptide_v8.2.fa \
Tetraodon_peptide_v8.2.fa.compo annotation_tetraodon_v8.2.gff
do
wget --timestamping "${D}/annotation_v8.2/${F}"
done
bunzip *.fa.bz2
gzip *.fa
##########################################################################
# Initial browser (DONE - 2009-08-06 - Hiram)
cd /hive/data/genomes/tetNig2
cat << '_EOF_' > tetNig2.config.ra
# Config parameters for makeGenomeDb.pl:
db tetNig2
clade vertebrate
scientificName Tetraodon nigroviridis
commonName Tetraodon
assemblyDate Mar. 2007
assemblyLabel Genoscope Tetraodon v8.0 (NCBI project 12350, CAAE01000000)
orderKey 459
mitoAcc NC_007176
fastaFiles /hive/data/genomes/tetNig2/genoscope/chr*.fa.gz
agpFiles /hive/data/genomes/tetNig2/genoscope/chr.agp
# qualFiles none
dbDbSpeciesDir tetraodon
taxId 99883
'_EOF_'
# << happy emacs
time nice -n +19 makeGenomeDb.pl -verbose=2 -workhorse=hgwdev \
-noGoldGapSplit -stop=agp tetNig2.config.ra > agp.log 2>&1
time nice -n +19 makeGenomeDb.pl -verbose=2 -workhorse=hgwdev \
-noGoldGapSplit -continue=db -stop=db tetNig2.config.ra > db.log 2>&1
time nice -n +19 makeGenomeDb.pl -verbose=2 -workhorse=hgwdev \
-noGoldGapSplit -continue=dbDb tetNig2.config.ra > dbDb.log 2>&1
# add the trackDb files to the source tree and entry to trackDb/makefile
##########################################################################
# Repeat Masker (DONE - 2009-08-06 - Hiram)
mkdir /hive/data/genomes/tetNig2/bed/repeatMasker
cd /hive/data/genomes/tetNig2/bed/repeatMasker
doRepeatMasker.pl -verbose=2 -workhorse=hgwdev \
-noSplit -buildDir=`pwd` tetNig2 > do.log 2>&1
cat faSize.rmsk.txt
# 358618246 bases (56303458 N's 302314788 real 292078336 upper 10236452 lower)
# in 27 sequences in 1 files
# %2.85 masked total, %3.39 masked real
# since this doesn't mask very much, use windowmasker instead
hgsql -e "drop table rmsk;" tetNig2
# this leaves the interrupted repeats track showing on genome-test
########################################################################
# Simple Repeats (DONE - 2009-08-06 - Hiram)
mkdir /hive/data/genomes/tetNig2/bed/simpleRepeat
cd /hive/data/genomes/tetNig2/bed/simpleRepeat
doSimpleRepeat.pl -workhorse=hgwdev \
-buildDir=`pwd` tetNig2 > do.log 2>&1 &
# fails on the job for chrM, make an empty result:
touch /hive/data/genomes/tetNig2/TrfPart/009/009.lst.bed
doSimpleRepeat.pl -workhorse=hgwdev -continue=filter \
-buildDir=`pwd` tetNig2 > filter.log 2>&1 &
cat fb.simpleRepeat
# 11549259 bases of 332311746 (3.475%) in intersection
########################################################################
# WindowMasker (DONE - 2009-08-06 - Hiram)
mkdir /hive/data/genomes/tetNig2/bed/windowMasker
cd /hive/data/genomes/tetNig2/bed/windowMasker
doWindowMasker.pl -workhorse=hgwdev -buildDir=`pwd` tetNig2 > do.log 2>&1
twoBitToFa tetNig2.wmsk.sdust.2bit stdout | faSize stdin
# 358618246 bases (56303458 N's 302314788 real 241249522 upper
# 61065266 lower) in 27 sequences in 1 files
# %17.03 masked total, %20.20 masked real
# load this initial data to get ready to clean it
ssh hgwdev
cd /hive/data/genomes/tetNig2/bed/windowMasker
hgLoadBed tetNig2 windowmaskerSdust windowmasker.sdust.bed.gz
# Loaded 1649525 elements of size 3
featureBits -countGaps tetNig2 windowmaskerSdust
# 117367586 bases of 358618246 (32.728%) in intersection
# eliminate the gaps from the masking
featureBits tetNig2 -not gap -bed=notGap.bed
time nice -n +19 featureBits tetNig2 windowmaskerSdust notGap.bed \
-bed=stdout | gzip -c > cleanWMask.bed.gz
# 91061086 bases of 332311746 (27.402%) in intersection
# reload track to get it clean
hgLoadBed tetNig2 windowmaskerSdust cleanWMask.bed.gz
# Loaded 1647549 elements of size 4
featureBits -countGaps tetNig2 windowmaskerSdust
# 91061086 bases of 358618246 (25.392%) in intersection
# mask the sequence with this clean mask
zcat cleanWMask.bed.gz \
| twoBitMask ../../tetNig2.unmasked.2bit stdin \
-type=.bed tetNig2.cleanWMSdust.2bit
twoBitToFa tetNig2.cleanWMSdust.2bit stdout | faSize stdin \
> tetNig2.cleanWMSdust.faSize.txt
cat tetNig2.cleanWMSdust.faSize.txt
# 358618246 bases (56303458 N's 302314788 real 241249522 upper 61065266
# lower) in 27 sequences in 1 files
# %17.03 masked total, %20.20 masked real
########################################################################
# MASK SEQUENCE WITH WM+TRF (DONE - 2009-08-06 - Hiram)
cd /hive/data/genomes/tetNig2
twoBitMask -add bed/windowMasker/tetNig2.cleanWMSdust.2bit \
bed/simpleRepeat/trfMask.bed tetNig2.2bit
# safe to ignore the warnings about BED file with >=13 fields
twoBitToFa tetNig2.2bit stdout | faSize stdin > faSize.tetNig2.txt
cat faSize.tetNig2.wmskSdust.TRF.txt
# 358618246 bases (56303458 N's 302314788 real 241039472 upper 61275316
# lower) in 27 sequences in 1 files
# %17.09 masked total, %20.27 masked real
# create symlink to gbdb
ssh hgwdev
rm /gbdb/tetNig2/tetNig2.2bit
ln -s `pwd`/tetNig2.2bit /gbdb/tetNig2/tetNig2.2bit
#########################################################################
# MAKE 11.OOC FILE FOR BLAT/GENBANK (DONE - 2009-08-06 - Hiram)
# Use -repMatch=130 (based on size -- for human we use 1024, and
# Tetraodon size is ~12.7% of human judging by gapless tetNig2 vs.
# hg18 genome size from featureBits.
# genome. Bump that up a bit to be more conservative.
# 100*302314788/2897310462 = 10.434324
cd /hive/data/genomes/tetNig2
blat tetNig2.2bit /dev/null /dev/null -tileSize=11 \
-makeOoc=jkStuff/tetNig2.11.ooc -repMatch=130
# Wrote 8132 overused 11-mers to jkStuff/tetNig2.11.ooc
# copy all of this stuff to the klusters:
cd /hive/data/genomes/tetNig2
mkdir /hive/data/staging/data/tetNig2
cp -p jkStuff/tetNig2.11.ooc chrom.sizes tetNig2.2bit \
/hive/data/staging/data/tetNig2
#########################################################################
# Ensembl genes v55 (DONE - 2009-08-06 - Hiram)
cd /hive/data/genomes/tetNig2
cat << '_EOF_' > tetNig2.ensGene.ra
# required db variable
db tetNig2
# optional nameTranslation, the sed command that will transform
# Ensemble names to UCSC names. With quotes just to make sure.
nameTranslation "s/^\([0-9XY][0-9]*\)/chr\1/; s/^MT/chrM/; s/^Un/chrUn/"
'_EOF_'
# << happy emacs
doEnsGeneUpdate.pl -verbose=2 -workhorse=hgwdev \
-ensVersion=55 -stop=process tetNig2.ensGene.ra > tetNig2.55.log 2>&1
doEnsGeneUpdate.pl -verbose=2 -workhorse=hgwdev \
-ensVersion=55 -continue=load tetNig2.ensGene.ra >> tetNig2.55.log 2>&1
featureBits tetNig2 ensGene
# 31637658 bases of 332311746 (9.520%) in intersection
+
+#########################################################################
+# BLATSERVERS ENTRY (DONE - 2009-08-06 - Hiram)
+Thu Aug 6 15:58:09 PDT 2009
+# After getting a blat server assigned by the Blat Server Gods,
+ ssh hgwdev
+
+ hgsql -e 'INSERT INTO blatServers (db, host, port, isTrans, canPcr) \
+ VALUES ("tetNig2", "blat15", "17794", "1", "0"); \
+ INSERT INTO blatServers (db, host, port, isTrans, canPcr) \
+ VALUES ("tetNig2", "blat15", "17795", "0", "1");' \
+ hgcentraltest
+ # test it with some sequence
+
+#########################################################################
+# Set default position same as tetNig1 after blating tetNig1 to here
+# (DONE - 2009-08-06 - Hiram)
+ hgsql -e \
+'update dbDb set defaultPos="chr10:2797091-2804214" where name="tetNig2";' \
+ hgcentraltest
+
#########################################################################