Tues. Jul. 23, 2019 Salmon + sea lice methylomes and Oyster Proteomics

Oyster Proteomics

Cleaned up the manuscript
- still think discussion and interpretation need work
  - would be good (and probably would be requested by reviewer) to compare to other proteomics results
    - found 3 papers that would make cool comparisons:

Salmon + sea lice methylomes

Still running TrimGalore! (probably will be around 30 hours to complete)
Prepared Bismark genomes on Mox:
- Salmon genome prep
  - script location: /gscratch/srlab/strigg/jobs/BuildSalmo_BmrkGenome.sh
  - bismark genome location: /gscratch/srlab/strigg/data/Ssalar/GENOMES
- Sea lice genome prep
  - script location: /gscratch/srlab/strigg/jobs/BuildCalig_BmrkGenome.sh
  - bismark genome location: /gscratch/srlab/strigg/data/Caligus/GENOMES
Determine bismark alignment settings to use
- Revisit past analysis:
  - I went back and did a quick but more thorough comparison
  - RESULTS here: https://github.com/shellywanamaker/C_virginica/blob/master/AlignementScoreComparison/BmrkAlignementScoreComparison.html
  - BmrkAlignementScoreComparison.Rmd code here: https://github.com/shellywanamaker/C_virginica/tree/master/AlignementScoreComparison
  - CONCLUSIONS:
    - I still think in this case AS 0,-1.2 -I 60 was the best compromise because it gives results closest to AS 0,-0.6 with a greater mapping effieciency (NOTE: mapping effieciency is the % of sequence pairs with unique alignments) and not much increase in artifical inflation of %C’s in CHH, CN or CHN, or CHG context.
    - I’m still not totally sure what we should be expecting for %C’s in CHH, CN or CHN, CHG, or CpG context, so that makes this whole analysis hard to wrap my head around.
  - NEXT STEPS:
    - I will try different parameters for the salmon/sea lice samples:
      - AS 0, -0.2
      - AS 0, -0.6
      - AS 0, -1
      - AS 0, -1 -I60
      - AS 0, -1.2 -I60
      - AS 0, -2
    - MOX scripts here: