May 2021 Goals

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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:

Other:

  • I paused work on the ocean acidification and reproduction review
  • Scheduled my defense! :o

May Goals

AKA rolling over April Goals that were rolled over from March

Hawaii Gigas Methylation:

  • Extract SNPs from bisulfite sequencing data with EpiDiverse
  • Complete preliminary assessment of DML with methylKit
  • Try identifying DML with DSS and ramwas
  • Compare ramwas and DSS DML output and determine which approach is suitable
  • Determine genomic location of DML
  • Identify overlaps between DML, SNP data, and other epigenomic data
  • Identify significantly enriched GOterms associated with DML
  • Identify methylation islands and non-methylated regions
  • Have a complete initial manuscript!
  • Send completed manuscript to my dissertation reading committee!

Gigas Gonad Methylation:

  • Extract SNPs from bisulfite sequencing data with EpiDiverse
  • Determine genomic location of DML
  • Identify overlaps between DML, SNP data, and other epigenomic data
  • Identify significantly enriched GOterms associated with DML
  • Identify methylation islands and non-methylated regions
  • Have a complete initial manuscript!
  • Decide if it’s worth extracting gonad RNA for integrated RNA-Seq and methylation analyses

Other:

  • Establish a dissertation reading committee
  • Finish all work on the ocean acidification and reproduction review
Written on May 3, 2021