Dinh 2011/NOTES/2011-10-7: Difference between revisions

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         #genomePrep.pl to stream-line reference genome preparation
         #genomePrep.pl to stream-line reference genome preparation
         #bisReadMapper to read in chromosome sizes
         #bisReadMapper to read in chromosome sizes
         October 13, 2011
         October 13, 2011
         #set all parameters with params.txt file [[File:sampleParams.txt]]
         #set all parameters with params.txt file [[File:sampleParams.txt]]
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         #generate a separate C-SNP bed file
         #generate a separate C-SNP bed file
         #option to call CHH and CHG methylation         
         #option to call CHH and CHG methylation         
         3. Make sure installation package works on a fresh computer
         3. Make sure installation package works on a fresh computer
         4. Include a better manual on how to use the program [[File:README.txt]]
         4. Include a better manual on how to use the program [[File:README.txt]]
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         Within samples, plot Watson vs Crick for H1, PGP1iPS, PGP1F in one figure
         Within samples, plot Watson vs Crick for H1, PGP1iPS, PGP1F in one figure
         Which samples to use for between batches ?
         Which samples to use for between batches ?
       
         1. Mention in main text
         1. Mention in main text
         2. Create supplementary figure or table
         2. Create supplementary figure or table

Revision as of 16:17, 13 October 2011

To-Do for Nature Methods revision on "Library-free Methylation Sequencing with Bisulfite Padlock Probes"

From Revision Document:

  1. LC Sciences Oligo Experiment - Noi
        1. Order primers for probe preparation - Dinh File:LC Sciences DMR Probes Design.pdf
  3. Package BisReadMapper correctly - Dinh
        1. Include SNP filtering script
        2. Make sure there are no errors in code
        ChangeNote:
        September 12, 2011
        #genomePrep.pl to stream-line reference genome preparation
        #bisReadMapper to read in chromosome sizes
        October 13, 2011
        #set all parameters with params.txt file File:SampleParams.txt
        #samtools mpileup output works with pileup2variantsStat
        #generate a separate C-SNP bed file
        #option to call CHH and CHG methylation         
        3. Make sure installation package works on a fresh computer
        4. Include a better manual on how to use the program File:README.txt
  4. Distribution of QC Metric within and between batches of samples- Dinh
        Within samples, plot Watson vs Crick for H1, PGP1iPS, PGP1F in one figure
        Which samples to use for between batches ?
        1. Mention in main text
        2. Create supplementary figure or table
  5. Analysis of capture performance - Dinh
        On HIV and African samples 
        1. # Unique CpGs targeted (overall)
        2. Sensitivity, Specificity, and Uniformity of Capture
             Sensitivity - probes capture efficiency plot
             Specific - % on/off target CpGs
             Uniformity - Show VennDiagram between batches number of CpG's unique and shared between batches
        3. Off-target sequencing/capture vs on-target
             Calculate reads mapped to target regions and those that don't
        4. Capture efficiency for each probe, subsetting/suppressors
             This is tied to capture sensitivity above
        5. Venn diagram illustrating overlap in coverage between two samples (H1 and PGP1F, for example)
  6. SNP Calilng in bisReadMapper - Dinh
        1. Mention that we can do this in main text briefly, and mention advantages (built-in genotyping)
        2. Add section to supplementary information on how this is performed; include some accuracy statistics on PGP1 and CV
  7. Clarifications - Everyone
        1. Improve line 79-82 (cis-interactions, long-range interactions)
              1. More clarification about GREAT vs true cis-interactions
        2. Cost analysis
              1. Clarify cost analysis (which costs we are including)
              2. Cost of probe libraries from LC Sciences
              3. Compare costs to RRBS and WGBS for different numbers of samples and targets
        3. Clarify difference between N2 protocol and library-free
              1. Mention advantages and disadvantages of each
              2. Clarify that CpGs covered - make it per megabase sequencing effort
        4. Clarify 100 bp PE vs 110 bp PE - mention CpGs covered per megabase
        5. Clarify statistical significance of DMRs
              1. Clarify that we only tested sites with more than 0.1 abs methylation difference, and that these were not statistically significantly different
              2. Mention that some sites had high absolute difference, but this was not statistically significant
        6. Emphasize the flexibility of our assay - we can target many different regions of interest
        7. Emphasize in bisReadMapper paragraph that we can map data of any bisulfite status in an unbaised manner; emphasize other novel aspects as well (including SNP calling)
  8. Upload correct probe set (H1, H2 sequences only for DMR330K) and target region file (206,312 regions) to website (include LC Sci probes and target region set) - Dinh