Rui:RNAseq analysis on HL109: Difference between revisions
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>RuiLiu m (Created page with '==HL109== * Samples: assumed to be HL106 [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui_Liu#HL106] ===Data=== * Transfer files less /home/ruiliu/SeqStore/111112_HL109/*_In…') |
>RuiLiu m (→Data) |
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===Data=== | ===Data=== | ||
* Transfer files | * Transfer files to Indx_seq folder, save as "less" batch command | ||
less /home/ruiliu/SeqStore/111112_HL109/*_Indx88.txt > Indx88.txt | 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 | |||
nohup 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 | |||
nohup 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 | |||
nohup 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 | |||
nohup 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 | |||
nohup 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 | |||
nohup 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 | |||
nohup 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 | |||
nohup 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 | |||
nohup 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 |
Revision as of 04:36, 21 November 2011
HL109
- Samples: assumed to be HL106 [1]
Data
- Transfer files to Indx_seq folder, save as "less" batch command
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
nohup 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 nohup 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 nohup 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 nohup 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 nohup 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 nohup 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 nohup 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 nohup 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 nohup 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