Rui:RNAseq analysis on Hiseq111005: Difference between revisions
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>RuiLiu |
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*[[Rui:Cufflinks 10.28.11|Cufflinks 10.28.11]] | *[[Rui:Cufflinks 10.28.11|Cufflinks 10.28.11]] | ||
*[[Rui:Matrix 10.30.11|Matrix 10.30.11]] | *[[Rui:Matrix 10.30.11|Matrix 10.30.11]] | ||
*[[Rui:Cufflinks_11.7.11|Cufflinks_11.7.11 w/ G annotation]] | |||
===Cufflinks_11.7.11 w/ G annotation=== | ===Cufflinks_11.7.11 w/ G annotation=== |
Revision as of 01:56, 22 November 2011
RNAseq analysis on Hiseq111005
Comparison of program
' | ' | Meangenemachine | Genome-miner | ' | ' |
Tophat | v1.3.1 | v1.3.1 | |||
Bowtie | 0.12.7.0 | 0.12.7.0 | |||
Samtools | 0.1.17 | 0.1.12a | |||
BowtieIndex | (UCSC) | (UCSC) | (Ensemble) | ||
.fa | 2011.8.8 | 2011.8.6 | 2011.10.27 | 2011.8.6 | |
.ebwt | 2011.5.16 | 2011.5.16 | 2011.9.27 | 2011.6.13 | |
Annotation | gene.gtf | 2011.5.17 | 2011.5.17 | 2011.9.27 | 2011.10.16 |
file | ~/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/gene.gtf | /GenomeDB/UCSC/Mus_musculus/mm9/Annotation/Genes/genes.gtf | ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/gene.gtf | /GenomeDB/MmGenome | |
cufflinks | v1.0.3 | v1.1.0 (2699) | |||
cuffdiff | v1.0.3 | v1.1.0 (2699) |
Data
- RNA libraries were used for HL101 run, Indx3-15, [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui_Liu#RNA_libraries_for_Dr._Yi_Zhang_lab
- Libraries to focus on is Indx9|10 (wt_m), Indx11|12 (wt_f), Indx13 (KO_m), Indx14|15 (KO_f)
- Data was stored in genome-miner:/media/Ext6T/111005_SN853/RNAseq
- make shortcut for input data:
ln -s /media/Ext6T/111005_SN853/RNAseq Hiseq111005/
- make a shorcut for output data:
ln -s /media/Ext4T/DataDrive.backup/RL_Scratch/RNAseq RNAseq/
- make copy of sequence file
cp Hiseq111005/* RNAseq/
- combine different files in different lanes into one file for each index:
less *Indx3.txt > Indx3.txt
- Transfer files to meangenemachine, as genome-miner is currently busy
ssh ruiliu@meangenemachine.dynamic.ucsd.edu scp ruiliu@genome-miner:~/RNAseq/Hiseq111005/Indx_seq/* ./
Tophat_10.25.11 w/o G correction
Tophat_10.27.11 w/ G correction
Cufflinks_11.7.11 w/ G annotation
- Previously, I used -g option which allows reference as the guide
- Dr. Zhang used -G option which excludes any novel transcripts
- To repeat cufflinks in genome-miner by using the following command
nohup /home/kunzhang/softwares/cufflinks-1.1.0.Linux_x86_64/cufflinks -G /GenomeDB/UCSC/Mus_musculus/mm9/Annotation/Genes/genes.gtf -N -p 2 -o Indx13 /home/ruiliu/RNAseq/Hiseq111005/tophat/Indx13_accepted_hits.bam > Indx13.log&
Problem need to solve: # can .bam file directly used for cufflinks? # is the tracking_id exactly same as gene_id?
--- genome-minor, bam file worked!
mkdir ~/RNAseq/Hiseq111005/cufflinks-G nohup /home/kunzhang/softwares/cufflinks-1.1.0.Linux_x86_64/cufflinks -G /GenomeDB/UCSC/Mus_musculus/mm9/Annotation/Genes/genes.gtf -N -p 2 -o Indx13 /home/ruiliu/RNAseq/Hiseq111005/tophat/Indx13_accepted_hits.bam > Indx13.log& nohup /home/kunzhang/softwares/cufflinks-1.1.0.Linux_x86_64/cufflinks -G /GenomeDB/UCSC/Mus_musculus/mm9/Annotation/Genes/genes.gtf -N -p 2 -o Indx14 /home/ruiliu/RNAseq/Hiseq111005/tophat/Indx14_accepted_hits.bam > Indx14.log& nohup /home/kunzhang/softwares/cufflinks-1.1.0.Linux_x86_64/cufflinks -G /GenomeDB/UCSC/Mus_musculus/mm9/Annotation/Genes/genes.gtf -N -p 2 -o Indx15 /home/ruiliu/RNAseq/Hiseq111005/tophat/Indx15_accepted_hits.bam > Indx15.log&
--- meangenemachine, bam file failed again!
nohup cufflinks -G ~/iGenome/ ~/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf -N -p 2 -o Indx13_cufflinks ~/Hiseq111005/Indx13/Indx13_tophat-G/accepted_hits.bam > Indx13.log&
Repeat RNAseq analysis on Hiseq111005 from 11.10.11
- Lesson 1: Use exactly same VERSION of programs/softwares to do analysis on ALL data in ONE computer
- Lesson 2: Random check for comparison
Tophat_11.10.11
- Genome-minor from 11:15am on 11.10.11
- Tophat 1.3.1
- Re-do on Indx 10, 11, 13, 14, 15, and 3
- move tophat folders into tophat_11.10.11
nohup tophat -p 3 --solexa1.3-quals -o Indx3 -G ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx3.txt & nohup tophat -p 3 --solexa1.3-quals -o Indx10 -G ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx10.txt & nohup tophat -p 3 --solexa1.3-quals -o Indx11 -G ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx11.txt & nohup tophat -p 3 --solexa1.3-quals -o Indx13 -G ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx13.txt & nohup tophat -p 3 --solexa1.3-quals -o Indx14 -G ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx14.txt & nohup tophat -p 3 --solexa1.3-quals -o Indx15 -G ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx15.txt &
Cufflinks_11.11.11
Cuffdiff_11.11.11
- UCSC gtf
nohup cuffdiff ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf -N -p 4 -o UCSC_cuffDiff_wtE13.5f_vs_KOE13.5f ../tophat_10.27.11/Indx6/Indx6_tophat/accepted_hits.bam,../tophat_11.10.11/Indx11/Indx11_tophat/accepted_hits.bam,../tophat_10.27.11/Indx12/Indx12_tophat/accepted_hits.bam ../tophat_11.10.11/Indx14/Indx14_tophat/accepted_hits.bam,../tophat_11.10.11/Indx15/Indx15_tophat/accepted_hits.bam & nohup cuffdiff ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf -N -p 4 -o UCSC_cuffDiff_wtE13.5m_vs_KOE13.5m ../tophat_10.27.11/Indx5/Indx5_tophat/accepted_hits.bam,../tophat_10.27.11/Indx9/Indx9_tophat/accepted_hits.bam,../tophat_11.10.11/Indx10/Indx10_tophat/accepted_hits.bam ../tophat_11.10.11/Indx13/Indx13_tophat/accepted_hits.bam &
- Emsemble gtf
nohup cuffdiff /GenomeDB/MmGenome/Mus_musculus.NCBIM37.chr.64.gtf -N -p 8 -o Ensemble_cuffDiff_wtE13.5f_vs_KOE13.5f ../tophat_10.27.11/Indx6/Indx6_tophat/accepted_hits.bam,../tophat_11.10.11/Indx11/Indx11_tophat/accepted_hits.bam,../tophat_10.27.11/Indx12/Indx12_tophat/accepted_hits.bam ../tophat_11.10.11/Indx14/Indx14_tophat/accepted_hits.bam,../tophat_11.10.11/Indx15/Indx15_tophat/accepted_hits.bam & nohup cuffdiff /GenomeDB/MmGenome/Mus_musculus.NCBIM37.chr.64.gtf -N -p 8 -o Ensemble_cuffDiff_wtE13.5m_vs_KOE13.5m ../tophat_10.27.11/Indx5/Indx5_tophat/accepted_hits.bam,../tophat_10.27.11/Indx9/Indx9_tophat/accepted_hits.bam,../tophat_11.10.11/Indx10/Indx10_tophat/accepted_hits.bam ../tophat_11.10.11/Indx13/Indx13_tophat/accepted_hits.bam &