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de novo Transcript Assembly

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Obi Griffith edited this page Nov 13, 2016 · 1 revision

RNA-seq Flowchart - Module 5

#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

| Previous Section | This Section | Next Section | |:---------------------------------------------------------:|:--------------------------------------------:|:--------------------------------------------:| | Ref Guided | De novo | Merging |

##Note: The current version of this tutorial is now at www.rnaseq.wiki

Table of Contents
Module 0: Authors | Citation | Syntax | Intro to AWS | Log into AWS | Unix | Environment | Resources
Module 1: Installation | Reference Genomes | Annotations | Indexing | Data | Data QC
Module 2: Adapter Trim | Alignment | IGV | Alignment Visualization | Alignment QC
Module 3: Expression | Differential Expression | DE Visualization
Module 4: Ref Guided | De novo | Merging | Differential Splicing | Splicing Visualization
Module 5: Kallisto
Appendix: Abbreviations | Lectures | Practical Exercise Solutions | Integrated Assignment | Proposed Improvements | AWS Setup

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