20230517
- Spent the day reorganizing, renaming, and documenting the E5 coral RNA/sRNA-seq data.
20230516
- Spent all day (seriously!) getting E5 coral RNA-seq data downloaded from Azenta via sFTP. SUPER ANNOYING!
20230515
Read Ch.6 of “Invisible Women”
Lab meeting
- Discussed Ch.6 of “Invisible Women”
Helped out Olivia with her RStudio Server issue
Downloaded Hollie Putnam coral sRNA-seq data from Azenta project 30-852430235.
- Download option is over sFTP, which constantly hangs. Requires constant monitoring and reconnecting/downloading. Very annoying.
CEABIGR meeting
- Not too much, as Steven and I discussed bisulfite SNP stuff on Friday at Science Hour. No Yaamini this week, so not much to talk about. Plus, Steven was at the hatchery.
20230512
Continued tweaking containerization testing.
Science Hour
- Steven at the hatchery.
20230511
Pub-a-thon
- Discussed bisulfite SNP analysis in more detail.
EpiDiverse/snppipeline might not be identifyingC > TSNPs like we want… Or, is that what we want?? Turns outEpiDiverse/snpmasks bisulfite conversions to allow for “normal” SNP analysis without the confounding factor of bisulfite conversions…
- Discussed bisulfite SNP analysis in more detail.
Worked on containerization.
20230510
- Spent most of the day thinking/messing around with bisulfite SNP calls. Even started a GitHub Discussion.
20230509
Ordered a bunch of stuff for Ariana.
Messed around with understanding bisulfite SNP calls using
bcftools.
20230508
Installed
ngsToolson Raven. (GitHub Issue)Lab Meeting
- Chris discussed eDNA project for the summer course she’s running.
CEABIGR meeting:
- Discussed/examined how to convert VCF to GLF (genome likelihood file).
Submitted E5 P.verrucosa Hisat2/StringTie/lncRNA script using older version of StringTie to avoid segmentation fault.
20230502
Helped reset a hanging Rstudio Server session which Celeste was having an issue with.
Wrote up a few notebook entries.
Finished Pacific geoduck (Panopea generosa) lncRNA identification.