Rui:Data Analysis: Difference between revisions
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==Examples== | ==Examples== | ||
KUN's pipeline: | |||
http://genome-tech.ucsd.edu/LabNotes/index.php/RNAseq_pipeline [http://genome-tech.ucsd.edu/LabNotes/index.php/RNAseq_pipeline] | |||
Jeff's samples: | Jeff's samples: | ||
Kun:LabNotes/Haplotyping/2010-9-17 [http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/Haplotyping/2010-9-17] | Kun:LabNotes/Haplotyping/2010-9-17 [http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/Haplotyping/2010-9-17] | ||
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Kun:LabNotes/Haplotyping/2011-6-14 [http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/Haplotyping/2011-6-14] | Kun:LabNotes/Haplotyping/2011-6-14 [http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/Haplotyping/2011-6-14] | ||
==Data analysis== | |||
*[[Rui:Haplotyping 6.21.11|Haplotyping 6.21.11]] | |||
*[[Rui:RNAseq analysis from 7.18.11|RNAseq analysis from 7.18.11]] | |||
*[[Rui:RNAseq analysis on HL098|RNAseq analysis on HL098]] | |||
*[[Rui:RNAseq analysis on HL099|RNAseq analysis on HL099]] | |||
*[[Rui:RNAseq analysis on HL101|RNAseq analysis on HL101]] | |||
*[[Rui:RNAseq analysis on Hiseq111005|RNAseq_PGCsamples on Hiseq111005]] | |||
*[[Rui:Hap analysis on HL108|Hap analysis on HL108]] | |||
*[[Rui:RNAseq analysis on HL109|RNAseq analysis on HL109]] | |||
*[[Rui:DNAseq analysis on HL114|DNAseq analysis on HL114]] | |||
*[[Rui:DNAseq analysis on Hiseq120313|DNAseq analysis on Hiseq120313]] | |||
*[[Rui:DNAseq analysis on HL118|DNAseq analysis on HL118]] | |||
*[[Rui:totoRNAseq on 121226_HL140|totoRNAseq on 121226_HL140]] | |||
*[[Rui:totoRNAseq on 130120_HL141|totoRNAseq on 130120_HL141]] | |||
*[[Rui:totoRNAseq on 130220_HL144|totoRNAseq on 130220_HL144]] | |||
*[[Rui:totoRNAseq on BL-UHRR-IVT-May28_2013|totoRNAseq on BL-UHRR-IVT-May28_2013]] | |||
*[[Rui:totoRNAseq on 131009_HL161|totoRNAseq on 131009_HL161]] | |||
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==RNAseq analysis key notes== | |||
* | * iGenome packages [http://tophat.cbcb.umd.edu/igenomes.html] | ||
# UCSC genome package: [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:Tophat_mapping_10.27.11] | |||
# Ensemble genome package: [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:Tophat_11.21.11#Re-download_Ensemble_package_from_iGenome_.5B1.5D] | |||
* Comparison of RNAseq analysis programs: [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:RNAseq_analysis_on_Hiseq111005#Comparison_of_program] | |||
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Latest revision as of 21:02, 31 October 2013
Examples[edit]
KUN's pipeline: http://genome-tech.ucsd.edu/LabNotes/index.php/RNAseq_pipeline [1]
Jeff's samples: Kun:LabNotes/Haplotyping/2010-9-17 [2]
Transcriptome: Kun:LabNotes/SingleCellExpr/2011-6-13 [3]
Haplotyping: Kun:LabNotes/Haplotyping/2011-6-14 [4]
Data analysis[edit]
- Haplotyping 6.21.11
- RNAseq analysis from 7.18.11
- RNAseq analysis on HL098
- RNAseq analysis on HL099
- RNAseq analysis on HL101
- RNAseq_PGCsamples on Hiseq111005
- Hap analysis on HL108
- RNAseq analysis on HL109
- DNAseq analysis on HL114
- DNAseq analysis on Hiseq120313
- DNAseq analysis on HL118
- totoRNAseq on 121226_HL140
- totoRNAseq on 130120_HL141
- totoRNAseq on 130220_HL144
- totoRNAseq on BL-UHRR-IVT-May28_2013
- totoRNAseq on 131009_HL161
RNAseq analysis key notes[edit]
- iGenome packages [5]
- Comparison of RNAseq analysis programs: [8]