Sam’s Notebook: Data Wrangling – Pgenerosa_v074.a3 Annotation Genome Feature Sequence Lengths

The GenSAS Pgenerosa_v074 annotation from 20190710 (referred to as: Panopea-generosa-vv0.74.a3) recently completed (after nearly a month of running).

In preparation for a paper we’re writing, we needed some summary stats for Panopea-generosa-vv0.74.a3. This info will be compiled in to a table for the manuscript. See our Genomic Resources wiki for more info on GFFs:

Calculations were performed using Python in a Jupyter Notebook.

Jupyter Notebook (GitHub):

Shelly’s Notebook: Fri. Aug. 30, 2019 Pt. Whitney Juvenile Exp. Setup

Adding 1.5 year old juveniles to experiment

tagged and took pictures of all animals

  • TRACKER: 2019_Var.low.pHxAmb_1.5yr_prevExposedJuveniles_TRACKER
  • Sequim animals:
    • ExE: uc?export=view&id=15gCFbbf28xUU9RX7WhYk1yiCcNs72lqz
    • ExA: uc?export=view&id=1B-S_05ovkudCzSO0pKY4HE_XTh46B-LB
    • AxE: uc?export=view&id=1NZAZYckWSq6ELYtCOekVOXdCQBpnl0q1
    • AxA: uc?export=view&id=1uh1x3iePHOnZuRwWfGwSWHAz2xipjDs-
  • Hatchery reared animals:
    • ExE: uc?export=view&id=15A3fjNMqmomkjEqG6nNwQFOp3HGbUEXM uc?export=view&id=1EUpWVQ4e0nKBIPSc0tJZhWwyUpQA1N_J
    • ExA: uc?export=view&id=1uhlrU7USSE8djp8gN8dnoSAqMqYrXdx6 uc?export=view&id=1au0-B9LdEsAI4FAEFfkKEnW1B84iDEpr
    • AxE: uc?export=view&id=1KprpEpWjw3I2ppB_IrUt7J2Tk1ulFEpD
      • we didn’t tag these 9 animals because we had no more tags
      • I forgot to take pictures of these next to the tape measure
    • AxA: uc?export=view&id=1pT_1V5uN_O_k6cj07PnVYAIw_slkhDf7 uc?export=view&id=1-X-uhUAbHfcEUR50ptCHKENgAhb453ZA
  • randomly split out groups across 4 silos containing about 1” of sand (2 replicate silos for ambient and 2 replicate silos for var.low pH)
    • Sequim ExE: 1 animal/silo
    • Sequim ExA: 1-2 animals/silo
    • Sequim AxE: 2-3 animals/silo
    • Sequim AxA: 1-2 animals/silo
    • Hatchery ExE: 2-3 animals/silo
    • Hatchery ExA: 2-3 animals/silo
    • Hatchery AxE: 2-3 animals/silo
    • Hatchery AxA: 2-3 animals/silo

Finishing experimental set-up

  • Calibrated discrete pH probe and measured discrete pH in tote 1:
    • mV = 23, pH = 6.6; so Apex probes are off
  • Calibrated all Apex probes:
    • PH-B1
    • PH-B2
    • PH-B3
    • PH-B5
  • further adjusted CO2 input by dialing back the black knob on the gas manifold
  • looked for manifold leaks and clogs. All looked good except on threaded adapter that was flowing slower than others. Unscrewed it and found leftover PVC shard from tapping that was clogging the port.
  • cleaned up manifold valve plumbing with new parts so it’s less complicated
  • cleaned silos that manila clams were in and stored on shelf near hatchery doorway
  • moved two heath trays with ambient and var.low pH progeny leftovers from H2 stack to raceway stack. Also put leftover hatchery reared 1.5 year old juveniles back in same spot: uc?export=view&id=1FgsM4QVP-U1OsaPmrrTTrXA1Gon8nANW
  • cleaned pumps and tubing that were going from ambient conical to manila clams and to H2 stack
  • took down remaining trays in H2 stack, including extras from setting since those trays barely had any live animals. I had stopped rotating those trays (H2-T6(var.low pH) and H2-T2(amb.)) since June 27 (see prevous posts: June 27 and July 24
  • finally, dropped off Liz’s supplies (clam gun, buckets, and PVC pipe pieces she lent us for the outplant we didn’t do) back at the Natural Resources Lab in Sequim and got back home around 6:30p.

Next Steps:

  • confirm Apex treatment with discrete measurment
  • develop sampling and respirometry plan for amb and var.low pH progeny
  • switch tote #2 onto treatment water

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