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View Blast2Go Maker-Augustus output RNASeq Cufflinks CLCAssemblyAll454HvCatIllum

First we selected the contigs from CLCAssemblyAll454HvCatIllum represented by RNASeq data and then use them to run Maker, the output of augustus (with organism saccharomyces cerevisiae_S288C) from maker run blast2Go

Split the file

fastasplit -f RNASeqCufflinksThirdHybridAssemblyCLC_saccharomyces_cerevisiae_S288C.augustus_up70.fasta -o RNASeqCufflinksThirdHybridAssemblyCLC_saccharomyces_cerevisiae_S288C.augustus_up70.fasta_chunks/ -c 32

Blast Vs Nr

for i in .; do blastall -p blastp -i $i -d /data/process/DBs/nr -e 1e-3 -o $i.VsNr.xml -m 7 -v 5 -b 5 & done

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