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View Process 006

Concatening ESTs Cenicafe with UnigenesBGI

cat ../Coffea_arabica-Unigene.oneline.fasta ESTsCenicafeCArabica.clean.fasta > BGIUnigenes_ESTsCenicafe_CAravica.fasta

Assembly with CAP3

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

grep -c ‘>’ ../Coffea_arabica-Unigene.oneline.fasta ->80790

cap3 BGIUnigenes_ESTsCenicafe_CArabica.fasta > BGIUnigenes_ESTsCenicafe_CArabica.fasta.cap3.out

grep -c ‘>’ BGIUnigenes_ESTsCenicafe_CArabica.fasta.cap.contigs ->18425

grep -c ‘>’ BGIUnigenes_ESTsCenicafe_CArabica.fasta.cap.singlets ->53280

Stastistics

/opt/scripts/CountFastaToStatistics.pl BGIUnigenes_ESTsCenicafe_CArabica.fasta.cap.contigs
Total length of sequence: 20189021 bp
Total number of sequences: 18425
N25 stats: 25% of total sequence length is contained in the 2369 sequences >= 1736 bp
N50 stats: 50% of total sequence length is contained in the 5781 sequences >= 1272 bp
N75 stats: 75% of total sequence length is contained in the 10484 sequences >= 908 bp
Total GC count: 8815363 bp
GC %: 43.66 %

Largest Contig

/opt/scripts/fastasize.pl BGIUnigenes_ESTsCenicafe_CArabica.fasta.cap.contigs | awk ‘{print $2}’ | sort -n -> 6470

Short Contig

/opt/scripts/fastasize.pl BGIUnigenes_ESTsCenicafe_CArabica.fasta.cap.contigs | awk ‘{print $2}’ | sort -n -r -> 139