Wed. Oct. 30, Geoduck DMR filtering

Summary of DMR analysis so far:

1. Call methylation state from bismark data (mox script here)
2. Call DMRs within individual samples (mox script here)
3. Filter DMRs for those in at least 3/4 samples/group (R script here, R proj here)
4. Filter DMRs for those significant at ANOVA uncorrected p.value < 0.1 R markdown script here, Rproj here

Summary of Step 4 above

Filtering DMRs for those significant at ANOVA uncorrected p.value < 0.1 from all 4 comparisons (all ambient samples, day10 samples, day 135 samples, and day 145 samples)

• R markdown here: Oct29_MCmax30DMR_group_stats.Rmd
  • ANOVA results:
    • amb_MCmax30_aov_modelsumm.csv
    • day10_MCmax30_aov_modelsumm.csv
    • day135_MCmax30_aov_modelsumm.csv
    • day145_MCmax30_aov_modelsumm.csv
• ANOVA significant all ambient MCmax30 DMR heatmap:
  • Heatmap key: Column color bar: light gray -> dark gray = day 0 -> day 145, heatmap cell color: Red = more methylation, blue = no methylation, black = no data.

• ANOVA significant all ambient MCmax30 DMR violinplots:

• ANOVA significant day 10 MCmax30 DMR heatmap:
  • Heatmap key: Column color bar: cyan = ambient, light pink = low.pH, magenta = super.low.pH. heatmap cell color: Red = more methylation, blue = no methylation, black = no data.

• ANOVA significant day 10 MCmax30 DMR violinplots:

• ANOVA significant day 135 MCmax30 DMR heatmap:
  • Heatmap key: Column color bar: cyan = ambient, light pink = low.pH, magenta = super.low.pH. heatmap cell color: Red = more methylation, blue = no methylation, black = no data.

• ANOVA significant day 135 MCmax30 DMR violinplots:

• ANOVA significant day 145 MCmax30 DMR heatmap:
  • Heatmap key: Column color bar: cyan = ambient, light pink = low.pH, magenta = super.low.pH. heatmap cell color: Red = more methylation, blue = no methylation, black = no data.
• ANOVA significant day 145 MCmax30 DMR violinplots:

Next steps:

• visualize significant DMRs in IGV
• Functional analysis of DMRs