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View Process Ca01

Mapping BGI Unigenes – Cenicafe Transcriptome Coffea Arabica Release 49

grep -c ‘>’ ../Coffea_arabica-Unigene.fa
56501

time megablast -i Coffea_arabica-Unigene.fa -d Coffea_Arabica_49.fasta -o Coffea_arabica-Unigene.faVsCoffea_Arabica_49.fasta.mblastW15 -W 15 -D 2 -p 100
real 41m38.477s
user 40m31.372s
sys 1m6.252s

time megablast -i Coffea_arabica-Unigene.fa -d Coffea_Arabica_49.fasta -o Coffea_arabica-Unigene.faVsCoffea_Arabica_49.fasta.mblastW18 -W 18 -D 2 -p 100
real 2m0.585s
user 1m47.007s
sys 0m6.944s

No Hits Found

grep -c ‘No hits found’ Coffea_arabica-Unigene.faVsCoffea_Arabica_49.fasta.megablastW15
135

grep -c ‘No hits found’ Coffea_arabica-Unigene.faVsCoffea_Arabica_49.fasta.mblastW18 23798

Extracting Unigenes that not mapped Coffea Arabica Release 49 – Cenicafe

grep -e ‘Query=’ -e ‘No hits found’ Coffea_arabica-Unigene.faVsCoffea_Arabica_49.fasta.megablast | grep -B 1 ‘No hits found’ | grep ‘Query=’ | awk ‘{print $2}’ > IdsCaUnigenesNotInCarabica_r49.txt

cdbfasta Coffea_arabica-Unigene.fa

cdbyank Coffea_arabica-Unigene.fa.cidx < IdsCaUnigenesNotInCarabica_r49.txt > CaUnigenesNotInCarabica_r49.fasta

time blastall -p blastx -i CaUnigenesNotInCarabica_r49.fasta -e 1e-5 -d /data/DBs/nr -o CaUnigenesNotInCarabica_r49.fastaVsNr.bx.xml -m 7 -v 20 -b 20 -a 2
real 123m46.601s
user 244m51.238s
sys 0m52.703s

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