Rui:RNAseq analysis on Hiseq111005: Difference between revisions

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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, Indx5-13, [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui_Liu#RNA_libraries_for_Dr._Yi_Zhang_lab
* 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:  
* 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:  
* 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
* make copy of sequence file
  cp Hiseq111005/* RNAseq/
  cp Hiseq111005/* RNAseq/
# combine different files in different lanes into one file for each index:  
* 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===
==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]

  • 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]


Tophat against Ensemble on 11.14.11[edit]