Rui:RNAseq analysis on Hiseq111005: Difference between revisions
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>RuiLiu m (Created page with '==RNAseq analysis on Hiseq111005]] ===Data=== * RNA libraries were used for HL101 run, Indx5-13, [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui_Liu#RNA_libraries_for_Dr._Yi…') |
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==RNAseq analysis on Hiseq111005] | ==RNAseq analysis on Hiseq111005== | ||
===Comparison of program=== | |||
{| {{table}} border=1 | |||
| align="center" style="background:#f0f0f0;"|'''''' | |||
| align="center" style="background:#f0f0f0;"|'''''' | |||
| align="center" style="background:#f0f0f0;"|'''Meangenemachine''' | |||
| align="center" style="background:#f0f0f0;"|'''Genome-miner''' | |||
| align="center" style="background:#f0f0f0;"|'''''' | |||
| align="center" style="background:#f0f0f0;"|'''''' | |||
|- | |||
| 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||[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)|||| | |||
|- | |||
| cuffdiff||||v1.0.3||v1.1.0 (2699)|||| | |||
|} | |||
===Data=== | ===Data=== | ||
* RNA libraries were used for HL101 run, | * 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 | * Data was stored in genome-miner:/media/Ext6T/111005_SN853/RNAseq | ||
* make shortcut for input data: | |||
ln -s /media/Ext6T/111005_SN853/RNAseq Hiseq111005/ | ln -s /media/Ext6T/111005_SN853/RNAseq Hiseq111005/ | ||
* make a shorcut for output data: | |||
ln -s /media/Ext4T/DataDrive.backup/RL_Scratch/RNAseq RNAseq/ | ln -s /media/Ext4T/DataDrive.backup/RL_Scratch/RNAseq RNAseq/ | ||
* make copy of sequence file | |||
cp Hiseq111005/* RNAseq/ | cp Hiseq111005/* RNAseq/ | ||
* combine different files in different lanes into one file for each index: | |||
less *Indx3.txt > Indx3.txt | 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=== | |||
*[[Rui:Tophat mapping|Tophat mapping]] | |||
*[[Rui:Transfer and convert files|Transfer and convert files]] | |||
*[[Rui:Cuffdiff|Cuffdiff]] | |||
*[[Rui:Cufflinks_10.26.11|Cufflinks_10.26.11]] | |||
*[[Rui:Matrix|Matrix]] | |||
===Tophat_10.27.11 w/ G correction=== | |||
*[[Rui:Tophat mapping 10.27.11|Tophat mapping 10.27.11]] | |||
*[[Rui:Cufflinks 10.28.11|Cufflinks 10.28.11]] | |||
*[[Rui:Matrix 10.30.11|Matrix 10.30.11]] | |||
*[[Rui:Cufflinks_11.7.11|Cufflinks_11.7.11 w/ G annotation]] | |||
==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 | |||
*[[Rui:Tophat_11.10.11|Tophat_11.10.11]] | |||
*[[Rui:Cufflinks_11.11.11|Cufflinks_11.11.11]] | |||
*[[Rui:Cuffdiff_11.11.11|Cuffdiff_11.11.11]] | |||
==Tophat against Ensemble on 11.14.11== | |||
*[[Rui:Tophat_11.14.11|Rui:Tophat_11.14.11]] | |||
*[[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