Shelly’s Notebook: Thur. Oct. 24, Geoduck DMR filtering

This analysis is a follow up to Wed. Oct 23 analysis

Rerun DMRfind with different parameters

Reran DMRfind with different MCmax settings (this specifies what a differentially methylated site (DMS) is; it allows loci to not be exactly be overlapping but be within a window to be considered a DMS which helps for low coverage samples). This window size is defined by MCmax:

Validate DMR bed files in IGV


  • Try running group stats on % methylation data and see if it excludes DMRs that don’t make sense
    • Yupeng confirmed that methylpy only runs statistics on within sample data, not on group data. So I need to apply an ANOVA or GLM to determine DMRs that are statistically different between groups