Rui:RNAseq analysis on HL109: Difference between revisions

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Line 14: Line 14:
  less /home/ruiliu/SeqStore/111112_HL109/*_Indx96.txt > Indx96.txt
  less /home/ruiliu/SeqStore/111112_HL109/*_Indx96.txt > Indx96.txt


===Tophat_11.20.11===
===Tophat_11.20.11 Mm folder===
* Using UCSC bowtieIndex and Annotation
* Using UCSC bowtieIndex and Annotation
* "tophat" batch command
* "tophat" batch command
Line 28: Line 28:
  tophat -p 10 --solexa1.3-quals -o Indx96 -G ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx96.txt
  tophat -p 10 --solexa1.3-quals -o Indx96 -G ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx96.txt


===Tophat_11.20.11===


===Re-download UCSC_Hs package from iGenome===
====Re-download UCSC_Hs package from iGenome====
  wget ftp://igenome:G3nom3s4u@ftp.illumina.com/Homo_sapiens/UCSC/hg19/Homo_sapiens_UCSC_hg19.tar.gz
  wget ftp://igenome:G3nom3s4u@ftp.illumina.com/Homo_sapiens/UCSC/hg19/Homo_sapiens_UCSC_hg19.tar.gz
  tar -zxvf Homo_sapiens_UCSC_hg19.tar.gz  
  tar -zxvf Homo_sapiens_UCSC_hg19.tar.gz  
Line 36: Line 37:
  Annotation: ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf
  Annotation: ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf


 
====Re-run tophat====
===Re-run tophat===
  tophat -p 10 --solexa1.3-quals -o Indx88 -G ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome ../Indx_seq/Indx88.txt  
  tophat -p 10 --solexa1.3-quals -o Indx88 -G ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome ../Indx_seq/Indx88.txt  
  tophat -p 10 --solexa1.3-quals -o Indx89 -G ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome ../Indx_seq/Indx89.txt
  tophat -p 10 --solexa1.3-quals -o Indx89 -G ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome ../Indx_seq/Indx89.txt
Line 46: Line 46:
  tophat -p 10 --solexa1.3-quals -o Indx94 -G ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome ../Indx_seq/Indx94.txt
  tophat -p 10 --solexa1.3-quals -o Indx94 -G ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome ../Indx_seq/Indx94.txt
  tophat -p 10 --solexa1.3-quals -o Indx95 -G ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome ../Indx_seq/Indx95.txt
  tophat -p 10 --solexa1.3-quals -o Indx95 -G ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome ../Indx_seq/Indx95.txt
====Stat.====
{| {{table}} border=1
| align="center" style="background:#f0f0f0;"|'''Hg19'''
| align="center" style="background:#f0f0f0;"|'''bowtie.log'''
| align="center" style="background:#f0f0f0;"|'''Indx88'''
| align="center" style="background:#f0f0f0;"|'''Indx89'''
| align="center" style="background:#f0f0f0;"|'''Indx90'''
| align="center" style="background:#f0f0f0;"|'''Indx91'''
| align="center" style="background:#f0f0f0;"|'''Indx92'''
| align="center" style="background:#f0f0f0;"|'''Indx93'''
| align="center" style="background:#f0f0f0;"|'''Indx94'''
| align="center" style="background:#f0f0f0;"|'''Indx95'''
|-
| ||processed||10,823,774||12,545,719||16,917,879||16,739,939||14,439,641||12,441,496||17,775,293||15,850,762
|-
| ||one alignment||6,030,520||7,206,915||9,344,109||9,210,627||8,199,746||7,211,466||8,315,444||6,324,495
|-
| ||||55.72%||57.45%||55.23%||55.02%||56.79%||57.96%||46.78%||39.90%
|-
| ||failed||4,761,793||5,293,227||7,540,575||7,511,226||6,224,057||5,203,180||9,424,809||9,498,774
|-
| ||||43.99%||42.19%||44.57%||44.87%||43.10%||41.82%||53.02%||59.93%
|-
| ||suppressed -m||31,461||45,577||33,195||18,086||15,838||26,850||35,040||27,493
|-
| ||||0.29%||0.36%||0.20%||0.11%||0.11%||0.22%||0.20%||0.17%
|-
| ||||||||||||||||||
|-
| Mm9||processed||10,823,774||12,545,719||16,917,879||16,739,939||14,439,641||12,441,496||17,775,293||15,850,762
|-
| ||one alignment||83,419||97,933||126,687||126,258||114,051||88,122||1,442,690||3,232,448
|-
| ||||0.77%||0.78%||0.75%||0.75%||0.79%||0.71%||8.12%||20.39%
|-
| ||failed||10,738,536||12,445,311||16,788,581||16,611,039||14,322,796||12,351,258||16,322,399||12,591,421
|-
| ||||99.21%||99.20%||99.24%||99.23%||99.19%||99.27%||91.83%||79.44%
|-
| ||suppressed -m||1,819||2,475||2,611||2,642||2,794||2,116||10,204||26,893
|-
| ||||0.02%||0.02%||0.02%||0.02%||0.02%||0.02%||0.06%||0.17%
|}


===Cuffdiff_11.22.11===
===Cuffdiff_11.22.11===

Revision as of 19:35, 23 November 2011

HL109

  • Samples: assumed to be HL106 [1]

Data

  • Transfer files to Indx_seq folder, save as "less" batch command, Indx92,95 and 96 were also used by Noi, repeat less
less /home/ruiliu/SeqStore/111112_HL109/*_Indx88.txt > Indx88.txt
less /home/ruiliu/SeqStore/111112_HL109/*_Indx89.txt > Indx89.txt
less /home/ruiliu/SeqStore/111112_HL109/*_Indx90.txt > Indx90.txt
less /home/ruiliu/SeqStore/111112_HL109/*_Indx91.txt > Indx91.txt
less /home/ruiliu/SeqStore/111112_HL109/*_Indx92.txt > Indx92.txt
less /home/ruiliu/SeqStore/111112_HL109/*_Indx93.txt > Indx93.txt
less /home/ruiliu/SeqStore/111112_HL109/*_Indx94.txt > Indx94.txt
less /home/ruiliu/SeqStore/111112_HL109/*_Indx95.txt > Indx95.txt
less /home/ruiliu/SeqStore/111112_HL109/*_Indx96.txt > Indx96.txt

Tophat_11.20.11 Mm folder

  • Using UCSC bowtieIndex and Annotation
  • "tophat" batch command
tophat -p 10 --solexa1.3-quals -o Indx88 -G ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx88.txt 
tophat -p 10 --solexa1.3-quals -o Indx89 -G ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx89.txt 
tophat -p 10 --solexa1.3-quals -o Indx90 -G ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx90.txt 
tophat -p 10 --solexa1.3-quals -o Indx91 -G ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx91.txt 
tophat -p 10 --solexa1.3-quals -o Indx92 -G ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx92.txt
tophat -p 10 --solexa1.3-quals -o Indx93 -G ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx93.txt  
tophat -p 10 --solexa1.3-quals -o Indx94 -G ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx94.txt 
tophat -p 10 --solexa1.3-quals -o Indx95 -G ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx95.txt 
tophat -p 10 --solexa1.3-quals -o Indx96 -G ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome ../Indx_seq/Indx96.txt

Tophat_11.20.11

Re-download UCSC_Hs package from iGenome

wget ftp://igenome:G3nom3s4u@ftp.illumina.com/Homo_sapiens/UCSC/hg19/Homo_sapiens_UCSC_hg19.tar.gz
tar -zxvf Homo_sapiens_UCSC_hg19.tar.gz 
BowtieIndex: ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome 
Annotation: ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf

Re-run tophat

tophat -p 10 --solexa1.3-quals -o Indx88 -G ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome ../Indx_seq/Indx88.txt 
tophat -p 10 --solexa1.3-quals -o Indx89 -G ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome ../Indx_seq/Indx89.txt
tophat -p 10 --solexa1.3-quals -o Indx90 -G ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome ../Indx_seq/Indx90.txt
tophat -p 10 --solexa1.3-quals -o Indx91 -G ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome ../Indx_seq/Indx91.txt
tophat -p 10 --solexa1.3-quals -o Indx92 -G ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome ../Indx_seq/Indx92.txt
tophat -p 10 --solexa1.3-quals -o Indx93 -G ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome ../Indx_seq/Indx93.txt
tophat -p 10 --solexa1.3-quals -o Indx94 -G ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome ../Indx_seq/Indx94.txt
tophat -p 10 --solexa1.3-quals -o Indx95 -G ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf ~/RNAseq/iGenome/UCSC_hg19/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome ../Indx_seq/Indx95.txt

Stat.

Hg19 bowtie.log Indx88 Indx89 Indx90 Indx91 Indx92 Indx93 Indx94 Indx95
processed 10,823,774 12,545,719 16,917,879 16,739,939 14,439,641 12,441,496 17,775,293 15,850,762
one alignment 6,030,520 7,206,915 9,344,109 9,210,627 8,199,746 7,211,466 8,315,444 6,324,495
55.72% 57.45% 55.23% 55.02% 56.79% 57.96% 46.78% 39.90%
failed 4,761,793 5,293,227 7,540,575 7,511,226 6,224,057 5,203,180 9,424,809 9,498,774
43.99% 42.19% 44.57% 44.87% 43.10% 41.82% 53.02% 59.93%
suppressed -m 31,461 45,577 33,195 18,086 15,838 26,850 35,040 27,493
0.29% 0.36% 0.20% 0.11% 0.11% 0.22% 0.20% 0.17%
Mm9 processed 10,823,774 12,545,719 16,917,879 16,739,939 14,439,641 12,441,496 17,775,293 15,850,762
one alignment 83,419 97,933 126,687 126,258 114,051 88,122 1,442,690 3,232,448
0.77% 0.78% 0.75% 0.75% 0.79% 0.71% 8.12% 20.39%
failed 10,738,536 12,445,311 16,788,581 16,611,039 14,322,796 12,351,258 16,322,399 12,591,421
99.21% 99.20% 99.24% 99.23% 99.19% 99.27% 91.83% 79.44%
suppressed -m 1,819 2,475 2,611 2,642 2,794 2,116 10,204 26,893
0.02% 0.02% 0.02% 0.02% 0.02% 0.02% 0.06% 0.17%

Cuffdiff_11.22.11

  • comparison for Wei:

[2]

  1. Indx88:91 - Ctrl/0d vs Ctrl/2d
  2. Indx89:92 - B1/0d vs B1/2d
  3. Indx90:93 - B3/0d vs B3/2d
  4. Indx88:89:90 - Ctrl/0d vs B1/0d vs B3/0d
  5. Indx91:92:93 - Ctrl/2d vs B1/2d vs B3/2d
  • comparison for Dr. Xu
  1. Indx94:95 - Ctrl vs RFP
  2. Indx94:96 - Ctrl vs RFP/GFP
  3. Indx95:96 - RFP vs GFP/RFP