Rui:Tophat 11.14.11

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Tophat_11.14.11[edit]

  • cuffdiff against Ensemble results in much less DE ~300 in E13.5f, ~100 in E13.5m
  • Repeat tophat against Ensemble gtf and Ensemble bowtie Index
nohup tophat -p 8 --solexa1.3-quals -o Indx15_E_E -G /GenomeDB/MmGenome/Mus_musculus.NCBIM37.chr.64.gtf /GenomeDB/MmGenome/mm9/mm9 ../Indx_seq/Indx15.txt &
nohup tophat -p 8 --solexa1.3-quals -o Indx15_E_U -G /GenomeDB/MmGenome/Mus_musculus.NCBIM37.chr.64.gtf ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx15.txt &
  • Use the original Ensemble gtf, nano "batch command", save as tophat_E_E.sh, sh tophat_E_E.sh
nohup tophat -p 2 --solexa1.3-quals -o Indx15 -G /GenomeDB/MmGenome/Mus_musculus.NCBIM37.64.gtf /GenomeDB/MmGenome/mm9/mm9 ../Indx_seq/Indx15.txt &
nohup tophat -p 2 --solexa1.3-quals -o Indx14 -G /GenomeDB/MmGenome/Mus_musculus.NCBIM37.64.gtf /GenomeDB/MmGenome/mm9/mm9 ../Indx_seq/Indx14.txt &
nohup tophat -p 2 --solexa1.3-quals -o Indx13 -G /GenomeDB/MmGenome/Mus_musculus.NCBIM37.64.gtf /GenomeDB/MmGenome/mm9/mm9 ../Indx_seq/Indx13.txt &
nohup tophat -p 2 --solexa1.3-quals -o Indx12 -G /GenomeDB/MmGenome/Mus_musculus.NCBIM37.64.gtf /GenomeDB/MmGenome/mm9/mm9 ../Indx_seq/Indx12.txt &
nohup tophat -p 2 --solexa1.3-quals -o Indx11 -G /GenomeDB/MmGenome/Mus_musculus.NCBIM37.64.gtf /GenomeDB/MmGenome/mm9/mm9 ../Indx_seq/Indx11.txt &
nohup tophat -p 2 --solexa1.3-quals -o Indx10 -G /GenomeDB/MmGenome/Mus_musculus.NCBIM37.64.gtf /GenomeDB/MmGenome/mm9/mm9 ../Indx_seq/Indx10.txt &
nohup tophat -p 2 --solexa1.3-quals -o Indx9 -G /GenomeDB/MmGenome/Mus_musculus.NCBIM37.64.gtf /GenomeDB/MmGenome/mm9/mm9 ../Indx_seq/Indx9.txt &
nohup tophat -p 2 --solexa1.3-quals -o Indx6 -G /GenomeDB/MmGenome/Mus_musculus.NCBIM37.64.gtf /GenomeDB/MmGenome/mm9/mm9 ../Indx_seq/Indx6.txt &
nohup tophat -p 2 --solexa1.3-quals -o Indx5 -G /GenomeDB/MmGenome/Mus_musculus.NCBIM37.64.gtf /GenomeDB/MmGenome/mm9/mm9 ../Indx_seq/Indx5.txt &
  • cuffdiff_11.20.11
nohup cuffdiff /GenomeDB/MmGenome/Mus_musculus.NCBIM37.64.gtf -N -p 10 -o Ensemble_cuffDiff_wtE13.5m_vs_KOE13.5m ../tophat_11.14.11/Indx5/accepted_hits.bam,../tophat_11.14.11/Indx9/accepted_hits.bam,../tophat_11.14.11/Indx10/accepted_hits.bam ../tophat_11.14.11/Indx13/accepted_hits.bam &
nohup cuffdiff /GenomeDB/MmGenome/Mus_musculus.NCBIM37.64.gtf -N -p 10 -o Ensemble_cuffDiff_wtE13.5f_vs_KOE13.5f ../tophat_11.14.11/Indx6/accepted_hits.bam,../tophat_11.14.11/Indx11/accepted_hits.bam,../tophat_11.14.11/Indx12/accepted_hits.bam ../tophat_11.14.11/Indx14/accepted_hits.bam,../tophat_11.14.11/Indx15/accepted_hits.bam &