Mussels, Mussels, and More Mussels

Mussel Methylation
Published

April 12, 2026

Plan of the Week: April 6 - April 12, 2026

High- level outline for the week. Adjusted daily to reflect progress of the day before

  • This week’s plan is to continue to move forward with the methylation analysis, refresh mutual goals, expectations and priorities with Steven, and set goals for April.

Monday - Planning the week & Setting April Goals

Tuesday - UW-RUA, No Science

Wednesday - Friday: Will Outline post Steven 1v1

Thursday - Task management

Friday - Biomarker Manuscript - ‘Clarify’ edits

Saturday - No Science

Sunday - Reading

Plan of the Day

Granular level task list to accomplish the high- level goal outlined above

  • Sunday’s original goal was to catch up on my reading re: methylation papers, but based on my upcoming week, I will shift to working on the biomarker manuscript and methylation analysis today instead.

Projects Touched Today

  • Mussel Methylation

Progress Notes

  • I started by updating the Methylation Project Log to include a page dedicated to questions and clarifications.
    • This is in conjunction with the rest of the project documentation to date. That project log can be found here.
    • The big goal is to keep as much documentation together as possible, so this is a test run for how it may operate.
  • Next, I set up the Agenda outline for my working session with Steven for Wednesday.
    • The Agenda is here - but definitely will not be complete until Tuesday.
  • I moved over to cleaning up and running the first methylKit script (06.0) to see if I know what I’m doing…
    • Before that, I added the context column to the metadata table
    • I had a feeling that I misinterpreted the methylKit code files from their original repos, and I was correct. So, I am going to make the following adjustments that match my current workflow without duplicating effort in any single script.
      • Up first, the most basic is to fix the titles of each script so that they are formatted properly.
      • Next, I’m going to adjust the setup. In 6.0-methylKit_import_and_qc, I’m going to also add the ‘unite’ step and PCA creation to put anything ‘data prep’ in the same script.
      • I put that together and started- or so I thought- I had to install methylkit first. Using Bioconductor and the documentation from the package site, it was a nice reminder that a perfect script doesn’t exist and you should probably check your tools as well! The time it takes to load the tools you could be working on the script.
      • That failed repeatedly because of the R version, the data.table package version, and a whole host of other issues that me & ChatGPT worked through, so I went to the GitHub install of methylKit via the al2na Github repo.
        • To do that, I had to install devtools - I feel like I’m constantly installing this - this is a sign that I need to do a little investigation at another time.
        • After devtools install and call, a whole host of things needed updating and then methylKit gave me hope…
        • Once this failed, I took a step back, rethought through the actual problem, and while staring at my screen was reminded that I built an environment to start work on my home device rather than the remote - it’s a container based in conda.
        • Pivoting to my existing environment, I tried to activate my conda environment - nothing, I tried mamba instead thinking I just forgot - wrong.
        • So, rather than fight the tide and keep trying to find these package version mismatches - which BTW were only the beginning problem - I am trying to remove the conflicts by ‘containing’ the work environment.
        • In terminal, I checked for both mamba and conda again, came up empty, and installed minimamba to go back to the controlled environment to try and install methylKit. It’s taking a bit, but once that is finished, I have a complete environment that should allow me to load methylKit- fingers crossed.
        • I lost it because I restarted R because renv() prompted it - this is uncool. Found it again, downloaded BiocManager again with the correct version. Got to methylKit - it failed.
        • This time the dependencies were the cause- PROGRESS!
        • I installed the other packages: c( “GenomicRanges”, “GenomeInfoDb”, “Rsamtools”, “fastseg”, “rtracklayer”, “Rhtslib”) and tried again.
        • None of that worked - I have literally tanked it at all troubleshooting or installation or whatever. That feels like time to take a break.
      • Following that, I’m going to put the DML and DMR code together into a single script, and then follow up with the tiles markdown.

Outcomes: Products & Word Count

  • Updated methylKit scripts: 3

Today’s total: 0 words

Monthly total to date: 4420 words

Annual total to date: 37,093 words

Annual target total to date: 50,500 words

Next Up: Tomorrow’s Plan

  • Biomarkers and methylation analysis.