I had such grand plans for Pubathon 2021 last month that obviously did not work out the way I thought. I made some good progress on the Hawaii and Manchester manuscripts! Talking to Steven, we also decided that those manuscripts will be the last components of my formal dissertation, so any additional labwork or projects are now firmly on the backburner until June. Hopefully this makes my plans for April more manageable (but knowing how I have not set reasonable goals since September 2016, jury’s still out on how this month will go).

March Goals Recap

I had some real LOFTY goals for last month.

Hawaii Gigas Methylation:

• Aligned samples to the Roslin genome! I proceeded with these alignments for the rest of my workflow after conducting some comparisons.
• I ran into some R memory issues working with methylKit, so I couldn’t identify pairwise DML. I was, however, able to look at global methylation patterns (not with Roslin alignments) I wrote up a plan in the methods section of my paper that I will execute when I shift this analysis to mox
• I looked into BS-Snper more, but haven’t identified SNPs yet! I had some samtools installation issues, but was able to install the necessary programs and merge BAM files in preparation for BS-Snper.
• Found an ATAC-Seq dataset, courtesy of one of Shelly’s friends!
• My methods section is up-to-date, and my results section is lagging a bit behind since I got the Roslin alignments later than expected
• Obtained WGS resequencing quote for UW, but I’m waiting on Genewiz

Gigas Gonad Methylation:

• I aligned samples to the Roslin genome, viewed data in IGV, and compared it to previous alignments
• Since I had R memory issues with the Hawaii dataset, I messed around with DML identification with the Manchester data. I successfully ran some code, but I still need to finish testing a few more chunks
• I’ve been more in analysis mode with this project, but I finally wrote up the DNA extraction methods.

Other:

• Reformatted and submitted the coral manuscript to MER and bioRxiv!
• Continued working on the ocean acidification and reproduction review, but as a last priority
• Submitted a peer review for Molecular Ecology
• Had a great vacation :)

April Goals

AKA a bunch of stuff rolled over from March.

Hawaii Gigas Methylation:

• Extract SNPs from bisulfite sequencing data with BS-SNPer and EpiDiverse
• Compare BS-SNPer and EpiDiverse output and determine which approach is suitable
• 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 significantly enriched GOterms associated with DML
• Identify methylation islands and non-methylated regions
• Have a complete initial manuscript!
• Obtain WGS resequencing quote from Genewiz

Gigas Gonad Methylation:

• Extract SNPs from bisulfite sequencing data with the method determined from Hawaii samples
• Identify DML using methylKit
• Determine genomic location of DML
• 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:

• Finish all work on the ocean acidification and reproduction review