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View Comparison Between Common and Unique Sequences in All Transcriptomes

Concatening All Trancriptomes

Working Directory bio@ticuna:/data/process/Roya/blastTransVsTrans

sed ‘s/>/>Hv701_/g’ ../blastTrancriptomVsNr/Hv701_Trans.fasta > Hv701Hv955HvCatNor.fasta
sed ‘s/>/>Hv955_/g’ ../blastTrancriptomVsNr/Hv955_Trans.fasta >> Hv701Hv955HvCatNor.fasta
sed ‘s/>/>HvCatNor_/g’ ../blastTrancriptomVsNr/HvCatNor955_Trans.fasta >> Hv701Hv955HvCatNor.fasta

grep -c ‘>’ Hv701Hv955HvCatNor.fasta
164840

blastall -p blastn -i Hv701Hv955HvCatNor.fasta -d Hv701Hv955HvCatNor.fasta -e 1e-100 -o blastTransVsTrans.bn.tab -m 8

Contigs in One Strain: 44784
Contigs in Two Strains: 43714
Contigs in Three Strains: 65308

Blast Contigs in One Strain Vs Nr

fastasplit -f HvTransIn1Strains.ids.fasta -o HvTransIn1Strains.ids.fasta_chunks/ -c 15

for i in .; do blastall -p blastx -i $i -d /data/process/DBs/nr -e 1e-5 -v 1 -b 1 -a 1 -m 7 -o $i.Vsnr.bx.xml & done

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