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de novo Transcript Assembly
######14. 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 Normal_cDNA1_lib2 --frag-len-mean 262 --frag-len-std-dev 80 --no-update-check $RNA_HOME/alignments/tophat/Normal_cDNA1_lib2/accepted_hits.bam
cufflinks -p 8 -o Normal_cDNA2_lib2 --frag-len-mean 262 --frag-len-std-dev 80 --no-update-check $RNA_HOME/alignments/tophat/Normal_cDNA2_lib2/accepted_hits.bam
cufflinks -p 8 -o Tumor_cDNA1_lib2 --frag-len-mean 262 --frag-len-std-dev 80 --no-update-check $RNA_HOME/alignments/tophat/Tumor_cDNA1_lib2/accepted_hits.bam
cufflinks -p 8 -o Tumor_cDNA2_lib2 --frag-len-mean 262 --frag-len-std-dev 80 --no-update-check $RNA_HOME/alignments/tophat/Tumor_cDNA2_lib2/accepted_hits.bam
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