Kun:LabNotes/SingleCellExpr/2011-10-6: Difference between revisions

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m (Created page with '==Repeat analysis of the 10 PD brain RNAseq data== ===Tophat mapping=== nohup /home/kunzhang/softwares/tophat-latest/tophat -p 4 --solexa1.3-quals -o 1741_tophat -G /GenomeD…')
 
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   nohup /home/kunzhang/softwares/tophat-latest/tophat -p 4 --solexa1.3-quals -o 5028_tophat  -G /GenomeDB/UCSC/Homo_sapiens/hg19/Annotation/Genes/genes.gtf  /GenomeDB/UCSC/Homo_sapiens/hg19/Sequence/BowtieIndex/genome 5028_cDNA_sequence.txt  > 5028.log&  
   nohup /home/kunzhang/softwares/tophat-latest/tophat -p 4 --solexa1.3-quals -o 5028_tophat  -G /GenomeDB/UCSC/Homo_sapiens/hg19/Annotation/Genes/genes.gtf  /GenomeDB/UCSC/Homo_sapiens/hg19/Sequence/BowtieIndex/genome 5028_cDNA_sequence.txt  > 5028.log&  
   nohup /home/kunzhang/softwares/tophat-latest/tophat -p 4 --solexa1.3-quals -o 5171_tophat  -G /GenomeDB/UCSC/Homo_sapiens/hg19/Annotation/Genes/genes.gtf  /GenomeDB/UCSC/Homo_sapiens/hg19/Sequence/BowtieIndex/genome 5171_cDNA_sequence.txt  > 5171.log&
   nohup /home/kunzhang/softwares/tophat-latest/tophat -p 4 --solexa1.3-quals -o 5171_tophat  -G /GenomeDB/UCSC/Homo_sapiens/hg19/Annotation/Genes/genes.gtf  /GenomeDB/UCSC/Homo_sapiens/hg19/Sequence/BowtieIndex/genome 5171_cDNA_sequence.txt  > 5171.log&
  /home/kunzhang/softwares/cufflinks-1.0.3.Linux_x86_64/cuffdiff /GenomeDB/UCSC/Homo_sapiens/hg19/Annotation/Genes/genes.gtf  \\
    -N -p 8 -o PD_vs_control 1741_tophat/accepted_hits.bam,1947_tophat/accepted_hits.bam,4526_tophat/accepted_hits.bam,4879_tophat/accepted_hits.bam,4977_tophat/accepted_hits.bam \\
    5028_tophat/accepted_hits.bam,5171_tophat/accepted_hits.bam,1818_tophat/accepted_hits.bam,4735_tophat/accepted_hits.bam,4789_tophat/accepted_hits.bam

Revision as of 23:03, 7 October 2011

Repeat analysis of the 10 PD brain RNAseq data

Tophat mapping

  nohup /home/kunzhang/softwares/tophat-latest/tophat -p 4 --solexa1.3-quals -o 1741_tophat   -G /GenomeDB/UCSC/Homo_sapiens/hg19/Annotation/Genes/genes.gtf  /GenomeDB/UCSC/Homo_sapiens/hg19/Sequence/BowtieIndex/genome 1741_cDNA_sequence.txt > 1741.log& 
  nohup /home/kunzhang/softwares/tophat-latest/tophat -p 4 --solexa1.3-quals -o 1818_tophat   -G /GenomeDB/UCSC/Homo_sapiens/hg19/Annotation/Genes/genes.gtf  /GenomeDB/UCSC/Homo_sapiens/hg19/Sequence/BowtieIndex/genome 1818_cDNA_sequence.txt  > 1818.log& 
  nohup /home/kunzhang/softwares/tophat-latest/tophat -p 4 --solexa1.3-quals -o 1947_tophat   -G /GenomeDB/UCSC/Homo_sapiens/hg19/Annotation/Genes/genes.gtf  /GenomeDB/UCSC/Homo_sapiens/hg19/Sequence/BowtieIndex/genome 1947_cDNA_sequence.txt  > 1947.log& 
  nohup /home/kunzhang/softwares/tophat-latest/tophat -p 4 --solexa1.3-quals -o 4526_tophat   -G /GenomeDB/UCSC/Homo_sapiens/hg19/Annotation/Genes/genes.gtf  /GenomeDB/UCSC/Homo_sapiens/hg19/Sequence/BowtieIndex/genome 4526_cDNA_sequence.txt  > 4526.log& 
  nohup /home/kunzhang/softwares/tophat-latest/tophat -p 4 --solexa1.3-quals -o 4735_tophat   -G /GenomeDB/UCSC/Homo_sapiens/hg19/Annotation/Genes/genes.gtf  /GenomeDB/UCSC/Homo_sapiens/hg19/Sequence/BowtieIndex/genome 4735_cDNA_sequence.txt  > 4735.log& 
  nohup /home/kunzhang/softwares/tophat-latest/tophat -p 4 --solexa1.3-quals -o 4789_tophat   -G /GenomeDB/UCSC/Homo_sapiens/hg19/Annotation/Genes/genes.gtf  /GenomeDB/UCSC/Homo_sapiens/hg19/Sequence/BowtieIndex/genome 4789_cDNA_sequence.txt  > 4789.log& 
  nohup /home/kunzhang/softwares/tophat-latest/tophat -p 4 --solexa1.3-quals -o 4879_tophat   -G /GenomeDB/UCSC/Homo_sapiens/hg19/Annotation/Genes/genes.gtf  /GenomeDB/UCSC/Homo_sapiens/hg19/Sequence/BowtieIndex/genome 4879_cDNA_sequence.txt  > 4879.log& 
  nohup /home/kunzhang/softwares/tophat-latest/tophat -p 4 --solexa1.3-quals -o 4977_tophat   -G /GenomeDB/UCSC/Homo_sapiens/hg19/Annotation/Genes/genes.gtf  /GenomeDB/UCSC/Homo_sapiens/hg19/Sequence/BowtieIndex/genome 4977_cDNA_sequence.txt  > 4977.log& 
  nohup /home/kunzhang/softwares/tophat-latest/tophat -p 4 --solexa1.3-quals -o 5028_tophat   -G /GenomeDB/UCSC/Homo_sapiens/hg19/Annotation/Genes/genes.gtf  /GenomeDB/UCSC/Homo_sapiens/hg19/Sequence/BowtieIndex/genome 5028_cDNA_sequence.txt  > 5028.log& 
  nohup /home/kunzhang/softwares/tophat-latest/tophat -p 4 --solexa1.3-quals -o 5171_tophat   -G /GenomeDB/UCSC/Homo_sapiens/hg19/Annotation/Genes/genes.gtf  /GenomeDB/UCSC/Homo_sapiens/hg19/Sequence/BowtieIndex/genome 5171_cDNA_sequence.txt  > 5171.log&
 /home/kunzhang/softwares/cufflinks-1.0.3.Linux_x86_64/cuffdiff /GenomeDB/UCSC/Homo_sapiens/hg19/Annotation/Genes/genes.gtf  \\
   -N -p 8 -o PD_vs_control 1741_tophat/accepted_hits.bam,1947_tophat/accepted_hits.bam,4526_tophat/accepted_hits.bam,4879_tophat/accepted_hits.bam,4977_tophat/accepted_hits.bam \\
   5028_tophat/accepted_hits.bam,5171_tophat/accepted_hits.bam,1818_tophat/accepted_hits.bam,4735_tophat/accepted_hits.bam,4789_tophat/accepted_hits.bam