Thur. Sept. 12, 2019 Geoduck Genome paper

Multi Sample BamQC

Generateed multi sample BamQC report with this jupyter notebook: https://github.com/shellywanamaker/Shelly_Pgenerosa/blob/master/analyses/MultiBamQC_allEPIsamples.ipynb

• report here: https://gannet.fish.washington.edu/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/multibamQC/multisampleBamQcReport.html

Geoduck genome 9/12 call:

• Decided we will focus on day10 comparison all groups
  • next week we will compare:
    • DMGs (Hollie)
    • DMLs (Steven)
    • DMRs (Shelly)
  • we will decide if analyses are redundant and if we should just go with one and then focus on the functional analysis
• one idea for TE analysis: compare TEs with DMRs to all TEs
  • is there a specific TE family that has DMRs?
• a method for plotting chromosomes with colored regions: karyoplotter
• methylation plotter (web interface Steven posted)