With Pubathon 2021 in full swing, I’ve been doing more writing (or at least, staring into the distance thinking about writing, then thinking about the analyses and work that comes before the writing, then panicking…)! My goals this month center around completing initial drafts of the Hawaii and Manchester, and setting myself up for new projects next quarter.

February Goals Recap

Hawaii Gigas Methylation:

• Evaluated bismark output using coral methylation workflow!
• I wasn’t able to look at the methylation with methylKit, but I’ve investigated a few packages (DSS and ramwas) to test out later
• Locate an ATAC-Seq dataset that could be used to practice integrating chromatin information with methylation
• Started drafting the manuscript!
• Investigated ways to identify SNPs from WGBS data

Gigas Gonad Methylation:

• Trimmed samples and evaulated with multiqc
• Aligned samples with bismark (but have yet to evaluate the output)
• I didn’t make it much farther than bismark!
• Made a Google Doc for the manuscript…but there are no words whoops

Virginica Labwork:

• Sent DNA and RNA for WGBS and RNA-Seq! I should receive samples at the end of March/beginning of April

ATAC-Seq Labwork:

• lol this is where the panicking happened

Other:

• Continued working on ocean acidification and reproduction review whenever I had time
• Completed my review for Evolutionary Applications (not Molecular Ecology I misspoke)
• Watched SICB talks and participated in a live discussion!

March Goals

Some very similar goals to last month, with a few additions.

Hawaii Gigas Methylation:

• Align samples to the Roslin genome and compare to previous alignments
• 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
• Locate an ATAC-Seq dataset that could be used to practice integrating chromatin information with methylation
• Have a complete initial manuscript
• Obtain WGS resequencing quote

Gigas Gonad Methylation:

• Align samples to the Roslin genome and compare to previous alignments
• 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
• Decide if it’s worth extracting gonad RNA for integrated RNA-Seq and methylation analyses
• Have a complete initial manuscript

ATAC-Seq Labwork:

• I’m tabling this work for now so I can focus on getting the other two projects in a good place by the end of the month!

Other:

• Submit ocean acidification and reproduction review
• Complete a peer review for Molecular Ecology
• Go on vacation :)