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View Process 008

Making blast PlantGDB Vs ESTsCenciafe

formatdb -i ESTsCenicafeCarabica.clean.fasta -p F -o T

blast -p blastn -i Coffea_arabica.mRNA.PUT.fasta -d ESTsCenicafeCarabica.clean.fasta -e 1e-5 -o Coffea_arabica.mRNA.PUT.fastaVsESTsCenicafeCarabica.clean.fasta.bn -v 20 -b 20 -a 16

grep -c ‘>’ ESTsCenicafeCarabica.clean.fasta -> 38858

grep -c ‘>’ Coffea_arabica.mRNA.PUT.fasta -> 49631

grep -c ‘No hists found’ Coffea_arabica.mRNA.PUT.fastaVsESTsCenicafeCarabica.clean.fasta.bn -> 9605

Making Blast PlantGDB Vs Hybrid Assembly

cat BGIUnigenes_ESTsCenicafe_CArabica.fasta.cap.contigs BGIUnigenes_ESTsCenicafe_CArabica.fasta.cap.singlets > BGIUnigenes_ESTsCenicafe_CArabica_contigs_singlets.fasta

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

grep -c ‘>’ BGIUnigenes_ESTsCenicafe_CArabica_contigs_singlets.fasta ->71705

blast -p blastn -i Coffea_arabica.mRNA.PUT.fasta -d BGIUnigenes_ESTsCenicafe_CArabica_contigs_singlets.fasta -e 1e-5 -o Coffea_arabica.mRNA.PUT.fastaVsBGIUnigenes_ESTsCenicafe_CArabica_contigs_singlets.fasta.bn -v 20 -b 20 -a 16

grep -c ‘No hists found’ Coffea_arabica.mRNA.PUT.fastaVsBGIUnigenes_ESTsCenicafe_CArabica_contigs_singlets.fasta.bn -> 0