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View Comparison Between Common and Unique Sequences in All Astrains

/data/process/Roya/assemblies/illuminaAssembly/CLCAssembly/HvVsHv$ cat HvStrain1…HvStrain8 > HvAllStrains.fasta

formatdb -i HvAllStrains.fasta -p F -o T

blastall -p blastn -i HvAllStrains.fasta -d HvAllStrains.fasta -e 1e-100 -o HvAllStrainsVsHvAllStrains.bn.tab -m8 -v 100 -b 100

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

upload HvAllStrainsVsHvAllStrains.bn.tab to table on database and make the query:

select qstrain,query_id, count(distinct sstrain)
from tmp.hvallstrainsvshvallstrains_bn
group by qstrain,query_id
having count(distinct sstrain)=8
7: Because are 8 Strains. Generating HvContigsInAllHvStrains.ids file.

cdbfasta HvAllStrains.fasta
1643442 entries from file HvAllStrains.fasta were indexed in file HvAllStrains.fasta.cidx

cdbyank HvAllStrains.fasta.cidx < HvContigsInAllHvStrains.ids > HvContigsInAllHvStrains.fasta

Comparison between common and unique sequences

Contigs in 8 Strains : 347715 File:HvContigsIn8Strains.zip
Contigs in 7 Strains : 209690 File:HvContigsIn7Strains.zip
Contigs in 6 Strains : 144756 File:HvContigsIn6Strains.zip
Contigs in 5 Strains : 110837 File:HvContigsIn5Strains.zip
Contigs in 4 Strains : 96979 File:HvContigsIn4Strains.zip
Contigs in 3 Strains : 93620 File:HvContigsIn3Strains.zip
Contigs in 2 Strains : 99778 File:HvContigsIn2Strains.zip
Contigs in 1 Strains : 186826 File:HvContigsIn1Strains.zip