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View Unique and shared contigs in CLC assemblies

Concatening All Tag Assemblies

cat ../Assemblies/Bb9001_Clean_CLC/Bb9001_Clean_CLCTag.fasta ../Assemblies/Bb9024_Clean_CLC/Bb9024_Clean_CLCTag.fasta ../Assemblies/Bb9119_Clean_CLC/Bb9119_Clean_CLCTag.fasta ../Assemblies/Bb9205_Clean_CLC/Bb9205_Clean_CLCTag.fasta > BbAllTag.fasta

grep -c ‘>’ BbAllTag.fasta
44932

blastall -i BbAllTag.fasta -d BbAllTag.fasta -e 1e-100 -o BbAllTagVsBbAllTag.bn.tab -m 8

/opt/scripts/tabToSql.pl BbAllTagVsBbAllTag.bn.tab > BbAllTagVsBbAllTag.bn.tab.sql

Executing query

select querystrain_id strain, queryid contig, count(distinct subjecstrainid) cantStrains
from tmp.“bballtagvsbballtag_bn”
where querystrain_id!=subjecstrainid
group by querystrain_id, queryid

File:BbContigsInStrains.xls

Statistics

wc -l contigOneStrain.ids 12177
wc -l contigTwoStrain.ids 3009
wc -l contigThreeStrains.ids 1874
wc -l contigFourStrains.ids 22979

Blast contigs in one strain vs Nr

time blastall -p blastx -i contigOneStrain.ids.fasta -d /data/process/DBs/nr -o contigOneStrain.ids.fastaVsNr.bx -v 10 -b 10 -e 1e-5 -a 2 &
real 9180m53.758s
user 12160m34.480s
sys 35m31.900s

Screen_shot_2012-03-05_at_12.24.59_PM.png

Screen_shot_2012-03-05_at_12.27.02_PM.png