Dinh Diep: Difference between revisions

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** [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-7-20] Analysis with EIGENSTAT software (population structure)
** [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-7-20] Analysis with EIGENSTAT software (population structure)
** [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-8-29] PCA
** [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-8-29] PCA
** [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-9-29] mQTL
** [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-2-21] Cleaning and repeat PCA
** [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-2-21] Cleaning and repeat PCA
** [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-2-27] Checking for reference genome bias
** [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-2-27] Checking for reference genome bias

Revision as of 00:26, 21 March 2012

Most recent meeting notes

  • [1] Updated March 16, 2012

Current Projects / Table of contents

  • bisReadMapper_v1
    • Developments:
  • Bisulfite Patch PCR (w/Michelle)
  • Memory/Mutation of iPSCs (Salk - Juan Carlos Lab, Sergio)
    • BSPP (Noi):

[4] 2nd batch (MSCs, hESCs) [5] 3rd batch, after differentiation

    • BSPP with N2 protocol (Dinh):

[6], [7] 1st batch

    • [8] Memory/mutation calling
    • [9] CpG localization
    • [10] [11] Localization with ChIP data
  • African Diversity - 48 Methylomes (UPenn collaboration, Sara/Laura)
    • BSPP (Noi):

[12] 1st batch [13] 2nd batch, tried to improve QC but they were all too low compared to previously assayed samples.

    • [14] Analysis with EIGENSTAT software (population structure)
    • [15] PCA
    • [16] mQTL
    • [17] Cleaning and repeat PCA
    • [18] Checking for reference genome bias
  • N37 individual, multiple tissues (Standard collaboration, Billy)
    • BSPP (Noi):

[19] 1st batch

    • [20] Genic methylation and expression levels
  • GA - (Glaucoma and optic atrophy?) (Kang Zhang lab)
    • BSPP (Noi):

[21] Noi did the experiment while also training two postdocs from Kang's lab.

    • [22] mQTL on 30 samples, SOM analysis
    • [23] PCA and HClust
  • Schizophrenia (UCLA, Tina and Dr. Roel)
    • BSPP (Noi):

[24] Noi did the experiment while also training Tina over the summer.

    • Sample identity - males versus females, [25]
    • Family background substraction, [26]
    • SibPair using TTest with family null data, [27]
    • Overlap SibPair with MPO, [28]
    • SNP Genetic distance plot, [29]
  • 5fC/5caC DIP-seq (University of Northern Carolina Medical School , Yi/Hao/Li)
    • Barcoding and sequencing (Alan):
    • [30] Genes Region Enrichment analysis, Biotin-labeled dIP
    • [31] Antibody dIP
    • [32] [33][34] Analysis at repeats
    • [35] 24 sets BOWTIE mapping
    • [36] [37] [38] [39] BWA PE mapping and peak calling
    • [40] RNA-seq - repeats mapping
  • Immunogeneticity and reprogramming (Yang Xu lab)
    • BSPP (Noi):

[41]


  • Breast Cancer and Diet (Richard, Moores Cancer Center UCSD)
    • Experiments were done in December 2009, January 2010, and February 2010.
    • [45] Paired Chi-square test
    • [46] [47] Compared resequenced datasets with old
    • [48] [49] mQTL
  • Methylation and metabolic genes
  • DMR330K probes
    • re-normalization: [51] Specificity measures, [52] Probes efficiency measures, [53] [54] Resubsetting strategy,
    • 9 Technical Replicates: [55] QC values, [56] [57] [58] Simulation of STDEV,
    • Random tagging of probes: [59] [60] [61]
    • [62] HMM to determine UMR, LMR, and HMR
  • Protocol optimizations:


  • Genemapster/Meangenemachine Updates
    • [80] Cuda EC
    • [81] Sanger methylation validation
    • [82] Installed upgrades
    • [83] New CUDA installation
    • [84] Test SOAP3 -- doesn't work on our GPU :(

Old projects

Slides

  • [86] 8-26-09 thru 9-28-09 Slides
  • [87] October 26, 2009 Slides
  • [88] November 23, 2009 Slides
  • [89] January 25, 2010 (short slides)
  • [90] March 8, 2010 CpG Methylation

Sequencing

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.

Notebook

<calendar> name=Dinh/Dinh_2012 format=%name/NOTES/%year-%month-%day date=2012/06/22 view=oneyear </calendar>

<calendar> name=Dinh_2011 format=%name/NOTES/%year-%month-%day date=2011/06/22 view=oneyear </calendar>

<calendar> name=Dinh format=%name/NOTES/%year-%month-%day date=2010/07/01 view=oneyear </calendar>