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arq5x/notes.md

Created Mar 8, 2017
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What would you like to do?
Jim's Thesis Talk
  1. State from the beginning that you are focusing on exome
  2. Talk through the pLI figure in more detail
  3. Any slide needs to talked through in detail if you present it
  4. Make it clear what missense variants are what you are seeing
  5. Should the observed CpG density be modulated by the codon content of the region
  6. Model ideas?
    • Exclude singletons???
    • use just synonymous density as the independent variable
  7. Molly Przezorski, CpG
  8. Simplify the explanation of each of the essential gene descriptions
    • use icons or pictures instead of Dickinson, et al, etc.
  9. Confounders
    • repeats
    • coverage
  10. Basic metrics about the model
  11. What is the distribution of number of top 1, 5, 10% CCRs per gene?
  12. What about looking at the ClinVar plot for variants in the ACMG genes?
  13. The pLI for NUP50 is 0.24
  14. Less is more.
  15. The science of writing
  16. Jim, let's take the input slide and try to correct it, then revisit it in a few days.
    • inputs in the model
    • heatmap slide
    • essential gene slide
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