Nov. 3-5, Salmon DMR analysis

Find DMRs

Filter DMRs

Group stats on DMRs

Data preprocessing:

  • To determine if there is a significant experimental effect on DMRs I first arcsin(sqrt) transformed the percent methylation data
  • BEFORE transformation percent methylation distribution:
    • AFTER transformation percent methylation distribution:

Run ANOVA

  1. I ran a 1 way ANOVA to test if sea lice infestation had an effect
    • 1 way ANOVA results summary table here: DMR_MCmax25_1wayAOV_infest_modelsumm.csv
    • 3 DMRs showed a significant infestation effect at 1way ANOVA p-value of < 0.01
    • 13 DMRs showed a significant infestation effect at 1way ANOVA p-value of < 0.05
    • 24 DMRs showed a significant infestation effect at 1way ANOVA p-value of < 0.1
      Heatmap of 24 DMRs that showed a significant infestation effect at 1way ANOVA p-value of < 0.1. Heatmap key:Column color bar in heat maps below: light pink = 16C_26psu, dark pink = 16C_32psu, light green = 8C_26psu, dark green = 8C_32psu, magenta = CTRL_16C_26psu, cyan = CTRL_8C_26psu. heatmap color: Red = more methylation, blue = no methylation, black = no data.
  2. For the 24 DMRs that showed a significant infestation effect at 1way ANOVA p-value of < 0.1, I ran a two way ANOVA on their percent methylation to see if temperature, salinity, or their interaction showed a significant effect.

Next steps

  • validate 24 DMRs that showed a significant infestation effect at 1way ANOVA p-value of < 0.1 in IGV
    • generate ANOVA filtered bed file
    • compare to filtered bam files linked above
  • find out where in the genome these DMRs are
Written on November 5, 2019