So…happy defense month I guess?

May Goals Recap

Hawaii Gigas Methylation:

• Characterized the methylation landscape!
• Identified DML with methylKit, and separately with DSS!
• Filtered my SNPs to only retain unique C/T SNPs
• Determined genomic location of DML, and overlaps between methylKit DML and SNPs, and did the same for DSS DML!
• I decided that using the EpiDiverse/snp workflow to identify SNPs was lower priority, so I didn’t tackle that
• I tried starting functional annotation for the Roslin genome, but encountered some struggles along the way. I should be able to resolve this quickly (hopefully)
• I don’t have a complete manuscript, but I have been diligently updating my methods and results with each analysis.

Gigas Gonad Methylation:

• Generated genome feature tracks for the Roslin genome!
• Characterized the methylation landscape
• Determine genomic location of DML and overlaps with SNP data
• I tried running randomization tests on mox, but was not successful. I think I identified mc.cores as the issue, and will report this to methylKit
• Kept updating the methods and results of my paper!

Other:

• Establish a dissertation reading committee
• Finish all work on the ocean acidification and reproduction review

June Goals

AKA rolling over May Goals that were rolled over from April…that were rolled over from March. One day I’ll learn how to set reasonable goals!

Hawaii Gigas Methylation:

• Extract SNPs from bisulfite sequencing data with EpiDiverse
• Identify significantly enriched GOterms associated with DML
• Identify methylation islands and non-methylated regions
• Finalize figures and statistical analyses
• Have a complete initial manuscript!
• Send completed manuscript to my dissertation reading committee no later than the end of the quarter!

Gigas Gonad Methylation:

• Identify significantly enriched GOterms associated with DML
• Identify methylation islands and non-methylated regions
• Finalize figures and statistical analyses
• Have a complete initial manuscript!
• Send completed manuscript to my dissertation reading committee no later than the end of the quarter!
• Decide if it’s worth extracting gonad RNA for integrated RNA-Seq and methylation analyses

Other:

• Finish all work on the ocean acidification and reproduction review
• Present at Chew Series seminar
• Draft defense talk for feedback from the lab
• DEFEND!
• Pass out for approximately six days