May 2021 Goals


Last month I encountered more struggles with R and methylKit than I anticipated…and did you know that not having DML is a bottleneck when you’re trying to understand methylation responses to ocean acidification?!??! Sigh. I made some progress that I think sets me up really well to finish my dissertation goals this month, so at least that’s good!

April Goals Recap

Hawaii Gigas Methylation:

  • I extracted SNPs from bisulfite sequencing data with BS-Snper! I have SNPs for each individual oyster, as well as SNPs from a merged BAM file. I didn’t get a chance to review SNP data or try EpiDiverse/snp just yet, but I have SNPs.
  • I didn’t work on getting DML from methylKit because I spent several weeks troubleshooting methylKit with the Manchester data. But, I have made progress on identifying a method!
  • Decided not to get a WGS resequencing quote from Genewiz since we already have one from UW, and UW is likely cheaper!

Gigas Gonad Methylation:


  • I paused work on the ocean acidification and reproduction review

May Goals

AKA rolling over April Goals that were rolled over from March

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from the responsible grad student