- 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?
- 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:
- decide which option to go for (look at with Steven)
- need to re-align newly trimmed data
- what parameters? maybe chat with Mac
- re-do DMR analysis
Geoduck reprod. paper: