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:

• Extracted SNPs with BS-Snper!
• Embarked on a SAGA to identify DML using methylKit, which included testing the base code, separating female and indeterminate samples, preparing a mox script, running R on mox in a SLURM script, calling an R script from a SLURM script, and finally, using the R Studio server. Now I have DML and a workflow!

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