Rui:Cufflinks: Difference between revisions
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>RuiLiu m (Created page with '====Cufflinks==== * genes.FPKM_tracking for each Indx is used to generate a matrix * prepare a matrix for gene set analysis cufflinks -g ~/iGenome/Mus_musculus/UCSC/mm9/Annotat…') |
>RuiLiu m (→Cufflinks) |
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==== | ====Cufflinks_10.31.11==== | ||
* genes.FPKM_tracking for each Indx is used to generate a matrix | * genes.FPKM_tracking for each Indx is used to generate a matrix | ||
* prepare a matrix for gene set analysis | * prepare a matrix for gene set analysis |
Latest revision as of 19:30, 10 November 2011
Cufflinks_10.31.11[edit]
- genes.FPKM_tracking for each Indx is used to generate a matrix
- prepare a matrix for gene set analysis
cufflinks -g ~/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf -o Indx5_cufflinks ../tophat_Indx5/tophat_out/accepted_hits.sam nohup cufflinks -g ~/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf -o Indx6_cufflinks ../tophat_Indx6/tophat_out/accepted_hits.sam & nohup cufflinks -g ~/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf -o Indx9_cufflinks ../tophat_Indx9/tophat_out/accepted_hits.sam & nohup cufflinks -g ~/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf -o Indx10_cufflinks ../tophat_Indx10/tophat_out/accepted_hits.sam & nohup cufflinks -g ~/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf -o Indx11_cufflinks ../tophat_Indx11/tophat_out/accepted_hits.sam & nohup cufflinks -g ~/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf -o Indx12_cufflinks ../tophat_Indx12/tophat_out/accepted_hits.sam & nohup cufflinks -g ~/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf -o Indx13_cufflinks ../tophat_Indx13/tophat_out/accepted_hits.sam & nohup cufflinks -g ~/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf -o Indx14_cufflinks ../tophat_Indx14/tophat_out/accepted_hits.sam & nohup cufflinks -g ~/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf -o Indx15_cufflinks ../tophat_Indx15/tophat_out/accepted_hits.sam &
nohup cufflinks -g ~/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf -o Indx3_cufflinks ../tophat_Indx3/tophat_out/accepted_hits.sam & nohup cufflinks -g ~/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf -o Indx4_cufflinks ../tophat_Indx4/tophat_out/accepted_hits.sam & nohup cufflinks -g ~/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf -o Indx7_cufflinks ../tophat_Indx7/tophat_out/accepted_hits.sam & nohup cufflinks -g ~/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf -o Indx8_cufflinks ../tophat_Indx8/tophat_out/accepted_hits.sam &
- Transfer to genome-miner
nohup scp -r ruiliu@meangenemachine.dynamic.ucsd.edu:~/Hiseq111005/cufflinks_UCSC ./cufflinks_UCSC