Rui:RNAseq analysis on HL109: Difference between revisions
Jump to navigation
Jump to search
>RuiLiu |
>RuiLiu |
||
Line 27: | Line 27: | ||
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:
- 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