Skip to content

de novo Transcript Assembly

Jump to bottom
Jason Walker edited this page Oct 7, 2016 · 17 revisions

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 cufflinks/de_novo
cd cufflinks/de_novo

cufflinks -p 8 -o HBR_Rep1 --no-update-check $RNA_HOME/alignments/hisat2/HBR_Rep1.bam
cufflinks -p 8 -o HBR_Rep2 --no-update-check $RNA_HOME/alignments/hisat2/HBR_Rep2.bam
cufflinks -p 8 -o HBR_Rep3 --no-update-check $RNA_HOME/alignments/hisat2/HBR_Rep3.bam

cufflinks -p 8 -o UHR_Rep1 --no-update-check $RNA_HOME/alignments/hisat2/UHR_Rep1.bam
cufflinks -p 8 -o UHR_Rep2 --no-update-check $RNA_HOME/alignments/hisat2/UHR_Rep2.bam
cufflinks -p 8 -o UHR_Rep3 --no-update-check $RNA_HOME/alignments/hisat2/UHR_Rep3.bam

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

NOTICE: This resource has been moved to rnabio.org. The version here will be maintained for legacy use only. All future development and maintenance will occur only at rnabio.org. Please proceed to rnabio.org for the current version of this course.

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: Alignment Free - Kallisto
Module 5: Ref Guided | De novo | Merging | Differential Splicing | Splicing Visualization
Module 6: Trinity
Module 7: Trinotate
Appendix: Saving Results | Abbreviations | Lectures | Practical Exercise Solutions | Integrated Assignment | Proposed Improvements | AWS Setup

Clone this wiki locally