Dinh Diep: Difference between revisions

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==Most recent meeting notes==
==Most recent meeting notes==
* [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-8-8] Thesis project (Updated August 8, 2012)
* [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-8-8] Thesis project (Updated August 8, 2012)
* [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-7-18] PGC WGBS/Rui (Updated July 19, 2012)
* [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-4-6] PNAS/Sergio (Updated 4/6/12)
* [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-1-27] BSPP Meeting (Updated March 16, 2012)
==Current Projects and Progress==
==Current Projects and Progress==
===Dinh's Projects===
===Dinh's Projects===
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   New version of code will use Bowtie2. NGS Mapper ROC curves: http://lh3lh3.users.sourceforge.net/alnROC.shtml
   New version of code will use Bowtie2. NGS Mapper ROC curves: http://lh3lh3.users.sourceforge.net/alnROC.shtml
   Run notes: [[dinh:COMPUTATIONAL/bisReadMapper]]
   Run notes: [[dinh:COMPUTATIONAL/bisReadMapper]]
* '''Bisulfite Patch PCR''' (w/Michelle)
[http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-11-4] Design
[http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-2-10] Consider SNPs


* '''DMR330K probes'''
* '''DMR330K probes'''
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  [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-7-28] New CUDA installation
  [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-7-28] New CUDA installation
  [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-12-7#SOAP3_.28latest_version.29] Test SOAP3 -- doesn't work on our GPU :(
  [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-12-7#SOAP3_.28latest_version.29] Test SOAP3 -- doesn't work on our GPU :(
* '''Bisulfite Patch PCR''' (w/Michelle)
[http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-11-4] Design
[http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-2-10] Consider SNPs


===Projects with Collaborators===
===Projects with Collaborators===
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**BSPP (Noi):[http://genome-tech.ucsd.edu/LabNotes/index.php/noi:Sample_tracking#May_25.2C_2011.2C_gDNA_of_10_different_tissues_from_Billi_Li.2C_Standforf_Univ] 1st batch
**BSPP (Noi):[http://genome-tech.ucsd.edu/LabNotes/index.php/noi:Sample_tracking#May_25.2C_2011.2C_gDNA_of_10_different_tissues_from_Billi_Li.2C_Standforf_Univ] 1st batch
  [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-10-3] Genic methylation and expression levels
  [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-10-3] Genic methylation and expression levels


* '''HAPMAP Study''' (Zhang lab, on grant proposal)
* '''HAPMAP Study''' (Zhang lab, on grant proposal)
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  SNP Genetic distance plot, [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-11-30]
  SNP Genetic distance plot, [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-11-30]
  Bis-SNP = more sensitive SNP calling, [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-9-22]
  Bis-SNP = more sensitive SNP calling, [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-9-22]
* '''African Diversity - 48 Methylomes''' (UPenn collaboration, Sara/Laura)
* '''African Diversity - 48 Methylomes''' (UPenn collaboration, Sara/Laura)
**BSPP (Noi):[http://genome-tech.ucsd.edu/LabNotes/index.php/noi:Sample_tracking#December_7.2C_2010_.28Sarah.27s_African_gDNA.2C_UPenn_.29] 1st batch [http://genome-tech.ucsd.edu/LabNotes/index.php/noi:Sample_tracking#September16.2C_2011.2C_received_3_more_gDNA_from_UPenn_to_repeat_the_capture_of_the_samples_with_low_QC_values] 2nd batch, tried to improve QC but they were all too low compared to previously assayed samples.
**BSPP (Noi):[http://genome-tech.ucsd.edu/LabNotes/index.php/noi:Sample_tracking#December_7.2C_2010_.28Sarah.27s_African_gDNA.2C_UPenn_.29] 1st batch [http://genome-tech.ucsd.edu/LabNotes/index.php/noi:Sample_tracking#September16.2C_2011.2C_received_3_more_gDNA_from_UPenn_to_repeat_the_capture_of_the_samples_with_low_QC_values] 2nd batch, tried to improve QC but they were all too low compared to previously assayed samples.
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===Finished/dropped projects===
===Finished/dropped projects===
* [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-7-18] PGC WGBS/Rui (Updated July 19, 2012)
* [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-4-6] PNAS/Sergio (Updated 4/6/12)
* [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-1-27] BSPP Meeting (Updated March 16, 2012)
* [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-10-7] Meeting notes/work for Nature Methods paper revision
* [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-10-7] Meeting notes/work for Nature Methods paper revision
* [[dinh:LAB/Bisulfite_Sequencing|Bisulfite Sequencing of CpG Sites (w/ Jie)]]
* [[dinh:LAB/Bisulfite_Sequencing|Bisulfite Sequencing of CpG Sites (w/ Jie)]]

Revision as of 20:58, 3 January 2013

Daily Lab Notebook

Notebook

Most recent meeting notes

  • [1] Thesis project (Updated August 8, 2012)

Current Projects and Progress

Dinh's Projects

  • bisReadMapper_v1
Developments:
 CpG/ChG/Chh position calling bugs fixed.
 New version of code will use Bowtie2. NGS Mapper ROC curves: http://lh3lh3.users.sourceforge.net/alnROC.shtml
 Run notes: dinh:COMPUTATIONAL/bisReadMapper
  • DMR330K probes
re-normalization: [2] Specificity measures, [3] Probes efficiency measures, [4] [5] Resubsetting strategy,
9 Technical Replicates: [6] QC values, [7] [8] [9] Simulation of STDEV, 
Random tagging of probes: [10] [11] [12]
Design new probes: [13] HMM to determine UMR, LMR, and HMR
  • Protocol optimizations:
[14] [15] Capture with 30K, 
[16] Capture with 97KA/B
[17] Multiplexing tests
[18] Multivariate capture with DMR220K
[19] N2-adapter 
[20] [21] BSPP [22] Training
[23] [24] Normalization capture
[25] [26] DMR220K + EXP1-3 Supressor oligos
[27] Design Probes for Single-End sequencing
[28] [29] [30] Circularization of probes
  • Genemapster/Meangenemachine Updates
[31] Cuda EC
[32] Sanger methylation validation
[33] Installed upgrades
[34] New CUDA installation
[35] Test SOAP3 -- doesn't work on our GPU :(
  • Bisulfite Patch PCR (w/Michelle)
[36] Design
[37] Consider SNPs

Projects with Collaborators

  • N37 individual, multiple tissues (Standard, Billy Li)
    • BSPP (Noi):[38] 1st batch
[39] Genic methylation and expression levels
  • HAPMAP Study (Zhang lab, on grant proposal)
    • BSPP (Noi): [40]
    • WGBS (Alan): ask Alan
Dealing with WGBS data [41] GM12878
Sequence dependent ASM [42] Binomial test and T-test
  • GA - (Glaucoma and optic atrophy?) (Kang Zhang lab)
    • BSPP (Noi): [43] Noi did the experiment while also training two postdocs from Kang's lab.
[44] mQTL on 30 samples, SOM analysis
[45] PCA and HClust
  • Schizophrenia (UCLA, Tina and Dr. Roel)
    • BSPP (Noi): [46] Noi did the experiment while also training Tina over the summer.
Sample identity - males versus females, [47]
Family background substraction, [48]
SibPair using TTest with family null data, [49]
Overlap SibPair with MPO, [50]
SNP Genetic distance plot, [51]
Bis-SNP = more sensitive SNP calling, [52]
  • African Diversity - 48 Methylomes (UPenn collaboration, Sara/Laura)
    • BSPP (Noi):[53] 1st batch [54] 2nd batch, tried to improve QC but they were all too low compared to previously assayed samples.
[55] Analysis with EIGENSTAT software (population structure)
[56] PCA
[57] mQTL
[58] Cleaning and repeat PCA
[59] Checking for reference genome bias
[60] Standardized CpGs quality filter using UPenn48 as an example.
  • 5fC/5caC DIP-seq (University of Northern Carolina Medical School , Yi/Hao/Li)
    • Barcoding and sequencing by Alan:
[61] Genes Region Enrichment analysis, Biotin-labeled dIP 
[62] Antibody dIP
[63] [64][65] Analysis at repeats
[66] 24 sets BOWTIE mapping
[67] [68] [69] [70] BWA PE mapping and peak calling
[71] RNA-seq - repeats mapping
  • Immunogeneticity and reprogramming (Yang Xu lab)
[73] [74] Memory/mutation calling
[75] Compare WGBS
  • Breast Cancer and Diet (Richard, Moores Cancer Center UCSD)
    • Experiments were done in December 2009, January 2010, and February 2010.
[76] Paired Chi-square test 
[77] [78] Compared resequenced datasets with old
[79] [80] mQTL
  • Methylation and metabolic genes
[81] Calculate DMS
  • Memory/Mutation of iPSCs (Salk - Juan Carlos Lab, Sergio)
    • BSPP (Noi): [82] 2nd batch (MSCs, hESCs) [83] 3rd batch, after differentiation
    • BSPP with N2 protocol (Dinh): [84], [85] 1st batch
[86] Memory/mutation calling
[87] CpG localization 
[88] [89] Localization with ChIP data

Finished/dropped projects

1. Perform quantification of libraries using PhiX 
2. Perform Cluster Generation and Sequencing, Protocol
3. Run pipeline modules for image analysis, base calling, and sequence alignment.

Slides

most recent ones at bottom