Mussel Methylation Analysis Return

Mussel Methylation
Published

March 20, 2026

Plan of the Week: March 16 - 22, 2026

  • I am feeling marginally better, and since I didn’t map the week on Sunday, the plan today is to keep it low key so I don’t put myself back at square one.
  • Monday: Map the week, catch up on UW-RUA work, confirm my spring/ summer tide schedule, build base histone and chromatin knowledge notes.
  • Tuesday: UW-RUA work, no science.
  • Wednesday: Return to epigenetic mechanisms to outline new Chapter 3 for my proposal.
  • Thursday: Biomarker manuscript
  • Friday: Biomarker manuscript
  • Saturday: Return to Chapter 3 outline and start drafting options for the introduction and methods.
  • Sunday: Continue Chapter 3 work.

Missing from the plan is the DNA Methylation work - it will be worked into the other priorities as time permits, or be a focus for spring break week next week.

Plan of the Day

  • Today’s goal was to work on biomarkers, but I am shifting to mussel methylation.
    • Because I am behind basically everywhere in every aspect of my life, I have a heavy task day. That equates to a lack of time to focus on deep work, the kind of work that I need to do with the biomarker manuscript.
    • I don’t want to not touch something science today, so I’m going to get something else cooking that is more formulaic going.

Projects Touched Today

  • Mussel Methylation

Progress Notes

  • My first step was to re-acclimate myself with where the project was in the pipeline, where it needed to go, and what the next tangible steps are.
    • First, I have not yet gotten myself sorted on Klone, so I am still working on Raven.
    • Reviewing the sequences and alignments, I realized three major things.
      • No documentation of matching checksums for my sequences or for the reference genome.
      • No notes on potential parameter testing/ mapping efficiency percentages and what was adjusted to get there, or what needed to be done.
      • I didn’t remove the sequencer artifacts from the work, so my QC reports are 99% unneccesary and not useful.
    • Since I just made a list of steps and decisions, I went back and used them!
      • First, I removed all of the old, second, I reviewed and updated the code files that I created from Steven’s originals and modified for running on my machine, not Raven. Most important, I added some echoes so I wasn’t flying blind in the process.
    • Next up, I cleaned up the repo folders, added code to concatenate the individual checksums into a single text file so I didn’t have to open 48 files…
      • Once my sequences were uploaded/ downloaded/ pulled into Raven, I pulled out one sample (reads 1 & 2) from the high PAH (69M) and low PAH (272M) to run through the complete process before analyzing the complete dataset.
      • I moved all other sequences out of the raw data folder and committed.

Products & Word Count

  • Updated code docs for QC, trimming, reference pull and alignment: ~100 words

Today’s total: 100 words

Monthly total to date: 8638 words

Annual total to date: 30,333 words

Annual target total to date: 39,500 words

Tomorrow’s Plan

  • Moving forward with the preliminary sequence run through QC, trimming, and alignment.
  • Continuing to knock out the other non-lab tasks and work I was not able to complete today.