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


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  scp ruiliu@genome-miner:~/RNAseq/Hiseq111005/Indx_seq/* ./
  scp ruiliu@genome-miner:~/RNAseq/Hiseq111005/Indx_seq/* ./


===Tophat===
===Tophat_10.25.11 w/o G correction===
* PATH issue from Athurva's note:
*[[Rui:Tophat mapping|Tophat mapping]]
ruiliu@genome-miner:~/RNAseq/Hiseq111005/tophat$ ~kunzhang/softwares/bowtie-latest/
*[[Rui:Transfer and convert files|Transfer and convert files]]
bowtie                bowtie-build-debug    bowtie-inspect        doc/                  indexes/              scripts/             
*[[Rui:Cuffdiff|Cuffdiff]]
bowtie-build          bowtie-debug          bowtie-inspect-debug  genomes/              reads/               
*[[Rui:Cufflinks_10.26.11|Cufflinks_10.26.11]]
ruiliu@genome-miner:~/RNAseq/Hiseq111005/tophat$ bowtie
*[[Rui:Matrix|Matrix]]
^C
 
ruiliu@genome-miner:~/RNAseq/Hiseq111005/tophat$ ls
===Tophat_10.27.11 w/ G correction===
nohup.out  tophat_Mm_Indx3
*[[Rui:Tophat mapping 10.27.11|Tophat mapping 10.27.11]]
ruiliu@genome-miner:~/RNAseq/Hiseq111005/tophat$ echo $PATH
*[[Rui:Cufflinks 10.28.11|Cufflinks 10.28.11]]
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
*[[Rui:Matrix 10.30.11|Matrix 10.30.11]]
ruiliu@genome-miner:~/RNAseq/Hiseq111005/tophat$ PATH=/home/kunzhang/softwares/
*[[Rui:Cufflinks_11.7.11|Cufflinks_11.7.11 w/ G annotation]]
abyss-1.2.5/                            Dindel/                                QuEST_2.4/
 
audy-stitch-db9e338/                    dindel-1.01-linux.tar.gz                QuEST_2.4.tar.gz
==Repeat RNAseq analysis on Hiseq111005 from 11.10.11==
audy-stitch-db9e338.tar.gz              dindel-1.01-python/                    README.txt
* Lesson 1: Use exactly same VERSION of programs/softwares to do analysis on ALL data in ONE computer
beagle.jar                              GenomeAnalysisTK-1.0.3864/              samtools-0.1.12a/
* Lesson 2: Random check for comparison
blast-2.2.20/                          GenomeAnalysisTK-1.0.4905/              samtools-0.1.7_x86_64-linux/
*[[Rui:Tophat_11.10.11|Tophat_11.10.11]]
blast-2.2.20-x64-linux.tar.gz          GenomeAnalysisTK-1.0.5083/              samtools-0.1.7_x86_64-linux.tar
*[[Rui:Cufflinks_11.11.11|Cufflinks_11.11.11]]
blat_34/                                GenomeAnalysisTK-latest/                samtools-latest/
*[[Rui:Cuffdiff_11.11.11|Cuffdiff_11.11.11]]
bowtie-0.12.7/                          GenomeAnalysisTK-latest.tar            SegSeq_1.0.1/
 
bowtie-latest/                          gm_key_64.tar                          SegSeq_1.0.1.tar.gz
 
brat-1.2.2/                            greatTools/                            SHERA/
==Tophat against Ensemble on 11.14.11==
brat-1.2.2.tar.gz                      greatTools.tar.gz                      SHERA_files.tar.gz
*[[Rui:Tophat_11.14.11|Rui:Tophat_11.14.11]]
bwa-0.5.8c/                            Homo_sapiens_UCSC_hg19.tar.gz          SNVMix2-0.11.8-r3/
*[[Rui:Tophat_11.21.11|Rui:Tophat_11.21.11]]
bwa-0.5.9/                              human_empty.bam                        SNVMix2-0.11.8-r3.tar.gz
bwa-0.5.9.tar                          impute_v2.1.2_x86_64_static.tgz        soap2.20release/
bwa-latest/                            jksrc/                                  SOAPdenovo_Release1.04/
cgatools-1.3.0.9-docs/                  jksrc.zip                              sratoolkit.2.1.6-centos_linux64/
cgatools-1.3.0.9-docs.tar.gz            macs_1.4.1.deb                          sratoolkit.2.1.6-centos_linux64.tar.gz
cgatools-1.3.0.9-linux-x86_64/          metaGene/                              stampy-1.0.8/
cgatools-1.3.0.9-linux-x86_64.tar.gz    MetaGeneMark_linux64/                  stampy-latest.tgz
cnver-0.7.2/                            MetaGeneMark_linux64.tar.gz            taoliu-MACS-7268e40/
cnver-0.7.2.tar.gz                      mga_ia64.tar                            taoliu-MACS-v2.0.7-11-g7268e40.tar.gz
CNVnator/                              ncbi-blast-2.2.24+/                    tophat-1.2.0.Linux_x86_64/
CNVnator_v0.2.2.zip                    OLB-1.8.0/                              tophat-1.3.1.Linux_x86_64/
cufflinks-1.0.3.Linux_x86_64/          OLB-1.9.3/                              tophat-1.3.1.Linux_x86_64.tar.gz
cufflinks-1.0.3.Linux_x86_64.tar.gz    OLB-1.9.3.tar.tar.gz                    tophat-latest/
cufflinks-1.1.0.Linux_x86_64/          Phrap/                                  trinityrnaseq_r2011-07-13/
cufflinks-1.1.0.Linux_x86_64.tar.gz    Phrap-distrib.tar.Z                    trinityrnaseq_r2011-07-13.tgz
cufflinks-latest/                      phred-dist-020425.c-acd.tar.Z          velvet_1.0.18/
Cython-0.15/                            picard-tools-1.38/                     
Cython-0.15.tar.gz                      picard-tools-latest/                   
ruiliu@genome-miner:~/RNAseq/Hiseq111005/tophat$ PATH=/home/kunzhang/softwares/^C
ruiliu@genome-miner:~/RNAseq/Hiseq111005/tophat$ PATH=/home/kunzhang/softwares/bowtie-latest:$PATH /home/kunzhang/softwares/tophat-latest/tophat -p 8 --solexa1.3-quals -o tophat_Mm_Indx3 -G /GenomeDB/UCSC/Mus_musculus/mm9/Annotation/Genes/genes.gtf /GenomeDB/UCSC/Mus_musculus/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx3.txt

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]