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View Process 004

ReAssembling ESTs CArabica Cenicafe with TGICL

Files: cleanSeqs.fasta.clean, cleanSeqs.qual.clean

/opt/tgicl_linux/tgicl cleanSeqs.fasta.clean -q cleanSeqs.qual.clean -O -p 95 -o 50 -y 20

/opt/tgicl_sunos/bin/cdbyank cleanSeqs.fasta.clean.cidx < cleanSeqs.fasta.clean.singletons > CArabicaSinContaminantes_singletons.fasta

grep -c ‘>’ CArabicaSinContaminantes_singletons.fasta ->19036
grep -c ‘>’ asm_1/contigs ->19822

Concatening Contigs + Singletons

cat CArabicaSinContaminantes_singletons.fasta asm_1/contigs > ESTsCenicafeCArabica.clean.fasta
grep -c ‘>’ ESTsCenicafeCArabica.clean.fasta ->38858

Changing name to specify cleanReads of C. arabica

mv ESTsCenicafeCArabica.clean.fasta ReadsCenicafeCArabica.clean.fasta