Sam's Notebook

Daily Bits - May 2023

by Sam White 1 min read

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/snp pipeline might not be identifying C > T SNPs like we want… Or, is that what we want?? Turns out EpiDiverse/snp masks bisulfite conversions to allow for “normal” SNP analysis without the confounding factor of bisulfite conversions…

  • Worked on containerization.

20230510

20230509

  • Ordered a bunch of stuff for Ariana.

  • Messed around with understanding bisulfite SNP calls using bcftools.

20230508

  • Installed ngsTools on 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