Differential Splicing

#5-iv. Differential Splicing Use Cuffdiff to compare the tumor and normal conditions. Refer to the Cufflinks manual for a more detailed explanation: http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff

Cuffdiff basic usage cuffdiff [options] <transcripts.gtf> <sample1_hits.sam> <sample2_hits.sam> [... sampleN_hits.sam] Supply replicate SAMs as comma separated lists for each condition: sample1_rep1.sam,sample1_rep2.sam,...sample1_repM.sam '-p 8' tells cuffdiff to use eight CPUs '-L' tells cuffdiff the labels to use for samples

For reference guided mode: cd $RNA_HOME/ mkdir -p de/tophat_cufflinks/ref_guided/ cd $RNA_HOME/alignments/tophat/

Perform Tumor vs. Normal comparison, using just the capture libraries, for known/novel (reference guided mode) transcripts cuffdiff -p 8 -L Normal,Tumor -o $RNA_HOME/de/tophat_cufflinks/ref_guided/ --frag-len-mean 262 --frag-len-std-dev 80 --no-update-check $RNA_HOME/expression/tophat_cufflinks/ref_guided/merged/merged.gtf Normal_cDNA1_lib2/accepted_hits.bam,Normal_cDNA2_lib2/accepted_hits.bam Tumor_cDNA1_lib2/accepted_hits.bam,Tumor_cDNA2_lib2/accepted_hits.bam

For de novo mode: cd $RNA_HOME/ mkdir de/tophat_cufflinks/de_novo/ cd $RNA_HOME/alignments/tophat/

Perform Tumor vs. Normal comparison, using just the capture libraries, for known/novel (de novo mode) transcripts cuffdiff -p 8 -L Normal,Tumor -o $RNA_HOME/de/tophat_cufflinks/de_novo/ --frag-len-mean 262 --frag-len-std-dev 80 --no-update-check $RNA_HOME/expression/tophat_cufflinks/de_novo/merged/merged.gtf Normal_cDNA1_lib2/accepted_hits.bam,Normal_cDNA2_lib2/accepted_hits.bam Tumor_cDNA1_lib2/accepted_hits.bam,Tumor_cDNA2_lib2/accepted_hits.bam