Rui:Cuffdiff
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Cuffdiff_10.26.11[edit]
genome-miner[edit]
- Cuffdiff comparison aganist Ensemble:
- /GenomeDB/MmGenome/Mus_musculus.NCBIM37.64.gtf only differs from UCSC gene.gtf in Chr. ID (eg. 8 vs Chr8)
- Dr. Zhang ran a script to change to Chr.ID
cd cuffdiff_Ensemble cuffdiff /GenomeDB/MmGenome/Mus_musculus.NCBIM37.64.gtf -N -p 8 -o cuffDiff_wtE13.5f_vs_KOE13.5f ../topha/Indx6_accepted_hits.sam,../tophat/Indx11_accepted_hits.sam,../tophat/Indx12_accepted_hits.sam ../tophat/Indx14_accepted_hits.sam,../tophat/Indx15_accepted_hits.sam cuffdiff /GenomeDB/MmGenome/Mus_musculus.NCBIM37.64.gtf -N -p 8 -o cuffDiff_wtE13.5m_vs_KOE13.5m ../tophat/Indx5_accepted_hits.sam,../tophat/Indx9_accepted_hits.sam,../tophat/Indx10_accepted_hits.sam ../tophat/Indx13_accepted_hits.sam
meangenemachine[edit]
- Cuffdiff comparison in UCSC:
cd cuffdiff_UCSC cuffdiff ~/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf -N -p 8 -o cuffDiff_wtE13.5f_vs_KOE13.5f ../tophat_Indx6/tophat_out/accepted_hits.bam,../tophat_Indx11/tophat_out/accepted_hits.bam,../tophat_Indx12/tophat_out/accepted_hits.bam ../tophat_Indx14/tophat_out/accepted_hits.bam,../tophat_Indx15/tophat_out/accepted_hits.bam cuffdiff ~/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf -N -p 8 -o cuffDiff_wtE13.5m_vs_KOE13.5m ../tophat_Indx5/tophat_out/accepted_hits.bam,../tophat_Indx9/tophat_out/accepted_hits.bam,../tophat_Indx10/tophat_out/accepted_hits.bam ../tophat_Indx13/tophat_out/accepted_hits.bam
- Transfer files in meangenemachine to laptop
scp ruiliu@meangenemachine.dynamic.ucsd.edu:~/Hiseq111005/cuffdiff_UCSC/cuffDiff_wtE13.5f_vs_KOE13.5f/gene_exp.diff ./Desktop/wtE13.5f_vs_KOE13.5f_gene_exp.diff_UCSC scp ruiliu@meangenemachine.dynamic.ucsd.edu:~/Hiseq111005/cuffdiff_UCSC/cuffDiff_wtE13.5m_vs_KOE13.5m/gene_exp.diff ./Desktop/wtE13.5m_vs_KOE13.5m_gene_exp.diff_UCSC
- Transfer files in genome-miner to laptop
scp ruiliu@genome-miner:~/RNAseq/Hiseq111005/cuffdiff_Ensemble/cuffDiff_wtE13.5f_vs_KOE13.5f/gene_exp.diff ./Desktop/wtE13.5f_vs_KOE13.5f_gene_exp.diff_ensemble scp ruiliu@genome-miner:~/RNAseq/Hiseq111005/cuffdiff_Ensemble/cuffDiff_wtE13.5m_vs_KOE13.5m/gene_exp.diff ./Desktop/wtE13.5m_vs_KOE13.5m_gene_exp.diff_ensemble