Rui:RNAseq analysis on Hiseq111005: Difference between revisions
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>RuiLiu |
>RuiLiu |
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| BowtieIndex||||(UCSC)||(UCSC)||||(Ensemble) | | BowtieIndex||||(UCSC)||(UCSC)||||(Ensemble) | ||
|- | |- | ||
| ||.fa||2011.8.8||2011.8.6||2011.10.27||2011. | | ||.fa||2011.8.8||2011.8.6||2011.10.27||2011.11.21 | ||
|- | |- | ||
| ||.ebwt||2011.5.16||2011.5.16||2011.9.27||2011. | | ||.ebwt||2011.5.16||2011.5.16||2011.9.27||2011.9.27 | ||
|- | |- | ||
| Annotation||gene.gtf||2011.5.17||2011.5.17||2011.9.27||2011. | | Annotation||gene.gtf||2011.5.17||2011.5.17||2011.9.27||2011.9.27 | ||
|- | |- | ||
| ||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||/ | | ||file||~/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/gene.gtf||/GenomeDB/UCSC/Mus_musculus/mm9/Annotation/Genes/genes.gtf||~/RNAseq/iGenome/UCSC/Mus_musculus/UCSC/mm9/Annotation/Genes/gene.gtf||[http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:Tophat_11.21.11#Tophat_11.21.11] | ||
|- | |- | ||
| cufflinks||||v1.0.3||v1.1.0 (2699)|||| | | cufflinks||||v1.0.3||v1.1.0 (2699)|||| | ||
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*[[Rui:Cuffdiff_11.11.11|Cuffdiff_11.11.11]] | *[[Rui:Cuffdiff_11.11.11|Cuffdiff_11.11.11]] | ||
==Tophat against Ensemble on 11.14.11== | ==Tophat against Ensemble on 11.14.11== | ||
*[[Rui:Tophat_11.14.11|Rui:Tophat_11.14.11]] | *[[Rui:Tophat_11.14.11|Rui:Tophat_11.14.11]] | ||
*[[Rui:Tophat_11.21.11|Rui:Tophat_11.21.11]] | *[[Rui:Tophat_11.21.11|Rui:Tophat_11.21.11]] |
Latest revision as of 18:07, 22 November 2011
RNAseq analysis on Hiseq111005[edit]
Comparison of program[edit]
' | ' | 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 | 2011.11.21 | |
.ebwt | 2011.5.16 | 2011.5.16 | 2011.9.27 | 2011.9.27 | |
Annotation | gene.gtf | 2011.5.17 | 2011.5.17 | 2011.9.27 | 2011.9.27 |
file | ~/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/gene.gtf | /GenomeDB/UCSC/Mus_musculus/mm9/Annotation/Genes/genes.gtf | ~/RNAseq/iGenome/UCSC/Mus_musculus/UCSC/mm9/Annotation/Genes/gene.gtf | [1] | |
cufflinks | v1.0.3 | v1.1.0 (2699) | |||
cuffdiff | v1.0.3 | v1.1.0 (2699) |
Data[edit]
- 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[edit]
Tophat_10.27.11 w/ G correction[edit]
Repeat RNAseq analysis on Hiseq111005 from 11.10.11[edit]
- 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
- Cufflinks_11.11.11
- Cuffdiff_11.11.11