Sam’s Notebook: Data Wrangling – Additional Features Stats for Panopea-generosa-v1.0

Although I’d previously generated some feature stats for this genome annotation (see 20191029), we decided we wanted to get some additional info, similar to that of Table 1 in M.Aranda et al 2016. Scientific Reports.

I’d previously created intron and intergenic features, but didn’t do any sort of analysis on them. In order to try to mirror some of what is in the table linked above, we need some stats from the introns file.

So, I generated some relevant stats with the introns file, as well as some other basic stats. Check out the deets in the Jupyter Notebook linked below.

Jupyter Notebook (GitHub):

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Shelly’s Notebook: 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: DMR_percmeth_hist.jpg
    • AFTER transformation percent methylation distribution: DMR_Tpercmeth_hist.jpg

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 DMR_MCmax25DMR_Taov0.01InfestPercMeth.jpg
    • 13 DMRs showed a significant infestation effect at 1way ANOVA p-value of < 0.05 DMR_MCmax25DMR_Taov0.05InfestPercMeth.jpg
    • 24 DMRs showed a significant infestation effect at 1way ANOVA p-value of < 0.1 DMR_MCmax25DMR_Taov0.1InfestPercMeth.jpg
      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. DMR_MCmax25DMR_Taov0.1_infest_heatmap.jpg
  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

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