Rui:Cuffdiff 11.11.11

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Cuffdiff_11.11.11[edit]

  • UCSC gtf
nohup cuffdiff ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf -N -p 4 -o UCSC_cuffDiff_wtE13.5f_vs_KOE13.5f ../tophat_10.27.11/Indx6/Indx6_tophat/accepted_hits.bam,../tophat_11.10.11/Indx11/Indx11_tophat/accepted_hits.bam,../tophat_10.27.11/Indx12/Indx12_tophat/accepted_hits.bam ../tophat_11.10.11/Indx14/Indx14_tophat/accepted_hits.bam,../tophat_11.10.11/Indx15/Indx15_tophat/accepted_hits.bam &
nohup cuffdiff ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf -N -p 4 -o UCSC_cuffDiff_wtE13.5m_vs_KOE13.5m ../tophat_10.27.11/Indx5/Indx5_tophat/accepted_hits.bam,../tophat_10.27.11/Indx9/Indx9_tophat/accepted_hits.bam,../tophat_11.10.11/Indx10/Indx10_tophat/accepted_hits.bam ../tophat_11.10.11/Indx13/Indx13_tophat/accepted_hits.bam &
  • Emsemble gtf
nohup cuffdiff /GenomeDB/MmGenome/Mus_musculus.NCBIM37.chr.64.gtf -N -p 8 -o Ensemble_cuffDiff_wtE13.5f_vs_KOE13.5f ../tophat_10.27.11/Indx6/Indx6_tophat/accepted_hits.bam,../tophat_11.10.11/Indx11/Indx11_tophat/accepted_hits.bam,../tophat_10.27.11/Indx12/Indx12_tophat/accepted_hits.bam ../tophat_11.10.11/Indx14/Indx14_tophat/accepted_hits.bam,../tophat_11.10.11/Indx15/Indx15_tophat/accepted_hits.bam &
nohup cuffdiff /GenomeDB/MmGenome/Mus_musculus.NCBIM37.chr.64.gtf -N -p 8 -o Ensemble_cuffDiff_wtE13.5m_vs_KOE13.5m ../tophat_10.27.11/Indx5/Indx5_tophat/accepted_hits.bam,../tophat_10.27.11/Indx9/Indx9_tophat/accepted_hits.bam,../tophat_11.10.11/Indx10/Indx10_tophat/accepted_hits.bam ../tophat_11.10.11/Indx13/Indx13_tophat/accepted_hits.bam &