Geoduck genome paper

Met with Steven and Sam today to recap our status


  • Start alignment for certain samples
    • maybe base this off samples that had the best coverage of v070 from this analysis or plot Steven’s data like here for coverage assessment of samples
    • OR just pick the same samples I already started analyzing on Emu and align them against v74 (day 145 amb-low and super.low-low samples: 205,206,214,215,220,221,226,and 227).
    • align to Steven’s v074 Bismark genome

Geoduck experiment planning

Met with Steven and Brent about experimental plans for Geoduck juveniles:

2019 Juveniles from conditioned brood

  • set up long term (2 months) pH exposure in totes
    • 2 x replicate totes for ambient
    • 2 x replicate totes for var low pH (same program as brood)
  • perform acute exposure to:
    • pH
    • temperature
    • salinity
    • lagoon water?
  • accute measurements:
    • measure respirometry directly in altered H2O?

Collecting remaining Sequim 2018 juveniles

  • When: possibly aug 28-30
    • Tides: Wed Aug 28 8:42am -1.58, Thu Aug 29 9:31am -1.74, Fri. Aug 30 10:17am -1.57
  • Who:
    • Need someone with stinger and pump to help retrieve animals (Brent will contact Jamestown about this)
  • Exp. plans:
    • possibly add these animals along side 2019 juveniles from conditioned broodstock in exposure experiments
  • NEED:
    • inventory of animals in the lab and in the field to see if we have enough from each treatment group
    • for dig up day: labeled containers to keep treatment groups separate and cooler to transport all back to pt. whitney
    • heath trays set up at Pt. Whitney to hold animals after transported back
  • Sam’s map and tracker for outplanted animals

Outplanting 2019 juveniles

  • When: day after retrieving 2018 juveniles
    • Can reuse tubes
  • Need labeling system and map