Meth compare:

  • work on piccard and qualimap figs
    • does data need to be subsetted for fig 3e?
  • update markdown with qualimap, lambda alignments, etc?
  • determine why different methods provide different methyaltion data
    • already know it’s not because symbiont homologous DNA
    • different cell types present?
      • can we survey for cell type specific SNPs (e.g. in germ cells?)
    • inter-individual variation?
      • what does RSD for %me of every loci look like?
  • should CpG coverage be normalized before comparing samples?
    • what is in the literature about this?
  • why does sample 8 have less methylation than others in the group? It has less sequencing, but why does that mean less me?
  • look at RRBS samples with CCGG tracks to see if cutting worked?

Geoduck Meth:

  • consolidate code
  • confirm flow of figs and supp
  • look into GO slim analysis / cluster by GOsemsim for biolgoical meaning of enriched DMG terms


  • integrate comments
  • build abstract
  • format for journal
  • make sure repo is clean

Sea lice methylome:

lab time

  • decide which option to go for (look at with Steven)

Salmon paper:

  • need to re-align newly trimmed data
    • what parameters? maybe chat with Mac
  • re-do DMR analysis

Geoduck reprod. paper:

Lab time

  • retake histology images with micrometer
  • restage slides
  • continue qPCR
  • manuscript draft:

Geoduck transgenerational paper:

  • manuscript draft:

Pteropod paper: