Rui:RNAseq analysis on HL109: Difference between revisions

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>RuiLiu
>RuiLiu
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  tophat -p 10 --solexa1.3-quals -o Indx95 -G ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx95.txt  
  tophat -p 10 --solexa1.3-quals -o Indx95 -G ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx95.txt  
  tophat -p 10 --solexa1.3-quals -o Indx96 -G ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx96.txt
  tophat -p 10 --solexa1.3-quals -o Indx96 -G ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx96.txt
===Cuffdiff_11.22.11===
* comparison for Wei:
[http://genome-tech.ucsd.edu/LabNotes/index.php/Rui_Liu#HL106.2FHL109]
# Ctrl/0d vs Ctrl/2d
# B1/0d vs B1/2d
# B3/0d vs B3/2d
# Ctrl/0d vs B1/0d vs B3/0d
# Ctrl/2d vs B1/2d vs B3/2d

Revision as of 18:48, 22 November 2011

HL109

  • Samples: assumed to be HL106 [1]

Data

  • Transfer files to Indx_seq folder, save as "less" batch command, Indx92,95 and 96 were also used by Noi, repeat less
less /home/ruiliu/SeqStore/111112_HL109/*_Indx88.txt > Indx88.txt
less /home/ruiliu/SeqStore/111112_HL109/*_Indx89.txt > Indx89.txt
less /home/ruiliu/SeqStore/111112_HL109/*_Indx90.txt > Indx90.txt
less /home/ruiliu/SeqStore/111112_HL109/*_Indx91.txt > Indx91.txt
less /home/ruiliu/SeqStore/111112_HL109/*_Indx92.txt > Indx92.txt
less /home/ruiliu/SeqStore/111112_HL109/*_Indx93.txt > Indx93.txt
less /home/ruiliu/SeqStore/111112_HL109/*_Indx94.txt > Indx94.txt
less /home/ruiliu/SeqStore/111112_HL109/*_Indx95.txt > Indx95.txt
less /home/ruiliu/SeqStore/111112_HL109/*_Indx96.txt > Indx96.txt

Tophat_11.20.11

  • Using UCSC bowtieIndex and Annotation
  • "tophat" batch command
tophat -p 10 --solexa1.3-quals -o Indx88 -G ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx88.txt 
tophat -p 10 --solexa1.3-quals -o Indx89 -G ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx89.txt 
tophat -p 10 --solexa1.3-quals -o Indx90 -G ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx90.txt 
tophat -p 10 --solexa1.3-quals -o Indx91 -G ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx91.txt 
tophat -p 10 --solexa1.3-quals -o Indx92 -G ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx92.txt
tophat -p 10 --solexa1.3-quals -o Indx93 -G ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx93.txt  
tophat -p 10 --solexa1.3-quals -o Indx94 -G ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx94.txt 
tophat -p 10 --solexa1.3-quals -o Indx95 -G ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx95.txt 
tophat -p 10 --solexa1.3-quals -o Indx96 -G ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx96.txt

Cuffdiff_11.22.11

  • comparison for Wei:

[2]

  1. Ctrl/0d vs Ctrl/2d
  2. B1/0d vs B1/2d
  3. B3/0d vs B3/2d
  4. Ctrl/0d vs B1/0d vs B3/0d
  5. Ctrl/2d vs B1/2d vs B3/2d