de novo Transcript Assembly

#4-ii. Cufflinks De Novo Mode Note, to discover novel transcripts with Cufflinks Using the alignments we generated in the previous modules we will now run Cuffinks in de novo mode To use de novo mode do not specify either of the '-G/--GTF' OR '-g/--GTF-guide' options.

cd $RNA_HOME/expression/
mkdir -p tophat_cufflinks/de_novo
cd tophat_cufflinks/de_novo

cufflinks -p 8 -o HBR_Rep1_ERCC-Mix2 --frag-len-mean 262 --frag-len-std-dev 80 --no-update-check $RNA_HOME/alignments/tophat/HBR_Rep1_ERCC-Mix2/accepted_hits.bam
cufflinks -p 8 -o HBR_Rep2_ERCC-Mix2 --frag-len-mean 262 --frag-len-std-dev 80 --no-update-check $RNA_HOME/alignments/tophat/HBR_Rep2_ERCC-Mix2/accepted_hits.bam
cufflinks -p 8 -o HBR_Rep3_ERCC-Mix2 --frag-len-mean 262 --frag-len-std-dev 80 --no-update-check $RNA_HOME/alignments/tophat/HBR_Rep3_ERCC-Mix2/accepted_hits.bam

cufflinks -p 8 -o UHR_Rep1_ERCC-Mix1 --frag-len-mean 262 --frag-len-std-dev 80 --no-update-check $RNA_HOME/alignments/tophat/UHR_Rep1_ERCC-Mix1/accepted_hits.bam
cufflinks -p 8 -o UHR_Rep2_ERCC-Mix1 --frag-len-mean 262 --frag-len-std-dev 80 --no-update-check $RNA_HOME/alignments/tophat/UHR_Rep2_ERCC-Mix1/accepted_hits.bam
cufflinks -p 8 -o UHR_Rep3_ERCC-Mix1 --frag-len-mean 262 --frag-len-std-dev 80 --no-update-check $RNA_HOME/alignments/tophat/UHR_Rep3_ERCC-Mix1/accepted_hits.bam

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