Rui:RNAseq analysis on Hiseq111005: Difference between revisions

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>RuiLiu
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*[[Rui:Transfer and convert files|Transfer and convert files]]
*[[Rui:Transfer and convert files|Transfer and convert files]]
*[[Rui:Cuffdiff|Cuffdiff]]
*[[Rui:Cuffdiff|Cuffdiff]]
*[[Rui:Cufflinks_10.31.11|Cufflinks_10.31.11]]
*[[Rui:Cufflinks_10.26.11|Cufflinks_10.26.11]]
*[[Rui:Matrix|Matrix]]
*[[Rui:Matrix|Matrix]]



Revision as of 19:31, 10 November 2011

RNAseq analysis on Hiseq111005

Data

  • 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 mapping 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
nohup tophat -p 3 --solexa1.3-quals -o Indx3_tophat-G -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_tophat-G -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_tophat-G -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_tophat-G -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_tophat-G -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_tophat-G -G ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx15.txt &