Rui:Tophat mapping 10.27.11

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Tophat mapping 10.27.11[edit]

  • Tophat against UCSC.gtf
nohup tophat -p 6 --solexa1.3-quals -o Indx15_tophat-G -G ~/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx15.txt &
nohup tophat -p 6 --solexa1.3-quals -o Indx14_tophat-G -G ~/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx14.txt &
nohup tophat -p 6 --solexa1.3-quals -o Indx13_tophat-G -G ~/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx13.txt &
nohup tophat -p 6 --solexa1.3-quals -o Indx12_tophat-G -G ~/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx12.txt &
nohup tophat -p 6 --solexa1.3-quals -o Indx11_tophat-G -G ~/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx11.txt &
nohup tophat -p 6 --solexa1.3-quals -o Indx10_tophat-G -G ~/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx10.txt &
  • genome-miner
Need to download UCSC dataset from iGenome to genome-miner
command: [1]
nohup tophat -p 6 --solexa1.3-quals -o Indx3_tophat-G -G /GenomeDB/UCSC/Mus_musculus/mm9/Annotation/Genes/genes.gtf /GenomeDB/UCSC/Mus_musculus/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx3.txt &
Others using newly download iGenome on genome-miner (~1hr download with wget, tar 20min) start at 1:40pm
nohup tophat -p 6 --solexa1.3-quals -o Indx4_tophat-G -G ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx4.txt &
nohup tophat -p 6 --solexa1.3-quals -o Indx5_tophat-G -G ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx5.txt &
nohup tophat -p 6 --solexa1.3-quals -o Indx6_tophat-G -G ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx6.txt &
nohup tophat -p 6 --solexa1.3-quals -o Indx7_tophat-G -G ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx7.txt &
nohup tophat -p 6 --solexa1.3-quals -o Indx8_tophat-G -G ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx8.txt &
nohup tophat -p 6 --solexa1.3-quals -o Indx9_tophat-G -G ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx9.txt &
nohup tophat -p 6 --solexa1.3-quals -o Indx12_tophat-G -G ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx12.txt &