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===Tophat_11.21.11=== ====Re-download Ensemble package from iGenome [http://tophat.cbcb.umd.edu/igenomes.html]==== wget ftp://igenome:G3nom3s4u@ftp.illumina.com/Mus_musculus/Ensembl/NCBIM37/Mus_musculus_Ensembl_NCBIM37.tar.gz tar -zxvf Mus_musculus_Ensembl_NCBIM37.tar.gz BowtieIndex: ~/RNAseq/iGenome/Ensemble/Mus_musculus/Ensembl/NCBIM37/Sequence/BowtieIndex/genome Annotation: ~/RNAseq/iGenome/Ensemble/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf ====Re-run tophat against Ensemble BowtieIndex and gtf==== * Use the Ensemble package, nano tophat_11.22.11.sh, nohup sh tophat_11.22.11.sh tophat -p 10 --solexa1.3-quals -o Indx15 -G ~/RNAseq/iGenome/Ensemble_NCBIM37/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Ensemble/Mus_musculus/Ensembl/NCBIM37/Sequence/BowtieIndex/genome ../Indx_seq/Indx15.txt tophat -p 10 --solexa1.3-quals -o Indx14 -G ~/RNAseq/iGenome/Ensemble_NCBIM37/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Ensemble/Mus_musculus/Ensembl/NCBIM37/Sequence/BowtieIndex/genome ../Indx_seq/Indx14.txt tophat -p 10 --solexa1.3-quals -o Indx13 -G ~/RNAseq/iGenome/Ensemble_NCBIM37/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Ensemble/Mus_musculus/Ensembl/NCBIM37/Sequence/BowtieIndex/genome ../Indx_seq/Indx13.txt tophat -p 10 --solexa1.3-quals -o Indx12 -G ~/RNAseq/iGenome/Ensemble_NCBIM37/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Ensemble/Mus_musculus/Ensembl/NCBIM37/Sequence/BowtieIndex/genome ../Indx_seq/Indx12.txt tophat -p 10 --solexa1.3-quals -o Indx11 -G ~/RNAseq/iGenome/Ensemble_NCBIM37/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Ensemble/Mus_musculus/Ensembl/NCBIM37/Sequence/BowtieIndex/genome ../Indx_seq/Indx11.txt tophat -p 10 --solexa1.3-quals -o Indx10 -G ~/RNAseq/iGenome/Ensemble_NCBIM37/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Ensemble/Mus_musculus/Ensembl/NCBIM37/Sequence/BowtieIndex/genome ../Indx_seq/Indx10.txt tophat -p 10 --solexa1.3-quals -o Indx9 -G ~/RNAseq/iGenome/Ensemble_NCBIM37/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Ensemble/Mus_musculus/Ensembl/NCBIM37/Sequence/BowtieIndex/genome ../Indx_seq/Indx9.txt tophat -p 10 --solexa1.3-quals -o Indx6 -G ~/RNAseq/iGenome/Ensemble_NCBIM37/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Ensemble/Mus_musculus/Ensembl/NCBIM37/Sequence/BowtieIndex/genome ../Indx_seq/Indx6.txt tophat -p 10 --solexa1.3-quals -o Indx5 -G ~/RNAseq/iGenome/Ensemble_NCBIM37/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Ensemble/Mus_musculus/Ensembl/NCBIM37/Sequence/BowtieIndex/genome ../Indx_seq/Indx5.txt ====Re-run cuffdiff_11.25.11==== * mkdir cuffdiff_11.25.11 * nano cuffdiff_11.25.11.sh, nohup sh cuffdiff_11.25.11.sh cuffdiff ~/RNAseq/iGenome/Ensemble_NCBIM37/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf -N -p 10 -o Ensemble_cuffdiff_wtE13.5m_vs_KOE13.5m ../tophat_11.21.11/Indx5/accepted_hits.bam,../tophat_11.21.11/Indx9/accepted_hits.bam,../tophat_11.21.11/Indx10/accepted_hits.bam ../tophat_11.21.11/Indx13/accepted_hits.bam cuffdiff ~/RNAseq/iGenome/Ensemble_NCBIM37/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf -N -p 10 -o Ensemble_cuffDiff_wtE13.5f_vs_KOE13.5f ../tophat_11.21.11/Indx6/accepted_hits.bam,../tophat_11.21.11/Indx11/accepted_hits.bam,../tophat_11.21.11/Indx12/accepted_hits.bam ../tophat_11.21.11/Indx14/accepted_hits.bam,../tophat_11.21.11/Indx15/accepted_hits.bam
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