Juvenile geoduck RRBS data analysis

  • FSH 546:
    • organize repo
    • Geoduck methylation analysis:
      • coverage
        • CpG methylation-what percentage of CpGs detected are methylated?
          • can get this info from:
            • Bismark methylation extractor
        • nucleotide coverage
          • Bismark nucleotide coverage report will plot % nucleotide coverage in sample and in genome. Expect sample and genome percentages to match

Geoduck Broodstock Experiment

  • Tritrator reagents to order:
    • Distilled (DI) water
    • pH Buffer 4.0 (Fisher SB101-4) Fisher pH4.0 buffer 4L (cat: SB101-4)
    • pH Buffer 7.0 (Fisher SB107-4) Fisher ph7.0 buffer 4L (cat: SB101-4)
    • pH buffer 10.0 (Fisher SB115-4) Fisher ph10.0 buffer 4L (cat: SB115-4)
    • 0.1M Hydrochloric acid from Dickson Lab Andrew Dickson 1 x 1000mL alkalinity titrant
    • check Hollie’s protocol against Pt. Whitney inventory