Rui:RNAseq analysis on HL109

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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


Re-download UCSC_Hs package from iGenome

wget ftp://igenome:G3nom3s4u@ftp.illumina.com/Homo_sapiens/UCSC/hg19/Homo_sapiens_UCSC_hg19.tar.gz
tar -zxvf Homo_sapiens_UCSC_hg19.tar.gz 
BowtieIndex: ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome 
Annotation: ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf


Re-run tophat

tophat -p 10 --solexa1.3-quals -o Indx88 -G ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome ../Indx_seq/Indx88.txt 
tophat -p 10 --solexa1.3-quals -o Indx89 -G ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome ../Indx_seq/Indx89.txt
tophat -p 10 --solexa1.3-quals -o Indx90 -G ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome ../Indx_seq/Indx90.txt
tophat -p 10 --solexa1.3-quals -o Indx91 -G ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome ../Indx_seq/Indx91.txt
tophat -p 10 --solexa1.3-quals -o Indx92 -G ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome ../Indx_seq/Indx92.txt
tophat -p 10 --solexa1.3-quals -o Indx93 -G ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome ../Indx_seq/Indx93.txt
tophat -p 10 --solexa1.3-quals -o Indx94 -G ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome ../Indx_seq/Indx94.txt
tophat -p 10 --solexa1.3-quals -o Indx95 -G ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome ../Indx_seq/Indx95.txt

Cuffdiff_11.22.11

  • comparison for Wei:

[2]

  1. Indx88:91 - Ctrl/0d vs Ctrl/2d
  2. Indx89:92 - B1/0d vs B1/2d
  3. Indx90:93 - B3/0d vs B3/2d
  4. Indx88:89:90 - Ctrl/0d vs B1/0d vs B3/0d
  5. Indx91:92:93 - Ctrl/2d vs B1/2d vs B3/2d
  • comparison for Dr. Xu
  1. Indx94:95 - Ctrl vs RFP
  2. Indx94:96 - Ctrl vs RFP/GFP
  3. Indx95:96 - RFP vs GFP/RFP