Daily Bits - December 2022 – Sam’s Notebook

Author

Sam White

Published

December 1, 2022

20221227

Read Ch.10 of “The Disordered Cosmos.”

20221221

Added transcriptome assembly info to The Handbook.

20221219

Finished notebook entries for Haws epidiverse/snp analysis using default config, as well as a run with a modified config file to compare runtimes. Spoiler: Default config file is significantly faster (less than half the runtime) than the modified config file I created.
Lab meeting:
- Matt talked about ANOVA stuff.
  - Provided helpful guide he wrote up.

20221216

Science Hour
- Looked through plottin Aidan’s crab data with Steven.
- Steven eventually utilized Weka machine learning to mess around wih Aidan’s data, too.

20221215

Ran epidiverse/snp pipeline on Haws’ lab C.gigas Hawaii BAM files for Yaamini. using the base config file to compare runtime to the modified config file I used yesterday.
- This actually completed in 12hrs, whereas the run using the modified config file took ~31hrs…
Pub-a-thon

20221214

Got epidiverse/snp pipeline on Haws’ lab C.gigas Hawaii BAM files for Yaamini.

20221213

Mox maintenance today slowed effort to run some jobs.
Worked on getting script/config files ready to run epidiverse/snp pipeline on Haws’ lab C.gigas Hawaii BAM files for Yaamini.

20221213

Read Ch.9 of “The Disordered Cosmos” for lab meeting.
Lab meeting.

20221209

Science Hour
- Worked extensively with Olivia and Steven regarding her citrate synthase assay data and analysis.

20221208

Participated in Katie Lotterhos workshop for designing Apps from Google Sheets.
Met with Linda Rhodes to discuss future of projects.
- Decision to cancel weekly meetings - will utilize GitHub issues instead.
- I’m going to try to figure out why new Silva 138 database doesn’t work as well as the old 132, in her pipeline.

20221207

Finally resolved CEABIGR mean methylation coefficient of methylation calcs (GitHub; R Markdown)! And, I figured it out in a very satisfactory, clean way! Looks great, easy to read, easy to follow, and concise.

20221202

Worked on CEABIGR mean methylation coefficient of variation stuff - getting frustrating, but getting closer!
Science Hour
CEABIGR meeting with Sam Brogan and Steven.

20221201

Worked on CEABIGR mean methylation coefficient of variation stuff - getting frustrating, but getting closer!
Helped Emma for awhile troubleshooting an issue with TrimGalore.