Shelly’s Notebook: Wed. Oct. 23, Geoduck DMR filtering

Rerun DMRfind with looser parameters

Reran DMRfind using loose parameters to be able to filter down by coverage in 3 samples/category

  • mox script here: 20191023_DMRfindAllEPI.sh
  • DMRfind parameters:
    • minimum coverage = 5 reads
    • mc-max dist = 50 bp (this specifies what a differentially methylated site is; I set this to 50 bp so that sites can be overlapping within a 50bp window to be considered which helps for low coverage samples)
    • dmr-max-dist = 250bp (this specifies the max size of the DMR)
    • min-num-dms = 3 (this specifies the number of DMS within a DMR required for the DMR to be called)
  • output files here: https://gannet.fish.washington.edu/metacarcinus/Pgenerosa/analyses/20191023/

Filter DMR output

Validate filtered DMRs

heatmaps of DMRs

  • markdown file here: Oct23_DMR_heatmaps.md
  • all ambient times (lighter – darker gray = Day 0 – Day 145): allAmb_DMR_heatmap-1.png
  • day 10 all pH (teal = ambient, light pink = low pH, dark pink = super low pH): day10_DMR_heatmap-1.png
  • day 135 all pH (teal = ambient, light pink = low pH, dark pink = super low pH): day135_DMR_heatmap-1.png
  • day 145 all pH (teal = ambient-ambient, light green = ambient-low pH, dark green = ambient-super low pH, purple = low-ambient, light pink = low-low, dark pink = low – superlow): day145_DMR_heatmap-1.png