Daily Bits - October 2022 | Sam’s Notebook

20221031

Lab meeting.
- Discussed Ch.6 of “The Disordered Cosmos”.
Worked on CEABIGR manuscript in preparation for Friday’s meeting with Kaite Lotterhos.

20221028

20221027

Worked on CEABIGR stuff - primarily creating a file of differences in max transcript counts between treatments/sexes for eventual use in Circos.
Pub-a-thon.
16s pipelines are still running! Mox job actually died a little after 1 day of running due a mistake I made in variable naming. Ugh. Restarted late tonight.

20221026

The 16s pipeline was still running after 24hrs. Decided this was too long, so killed it.
- Ran Linda Rhodes’ 16s pipeline with the reduced 138.99 515-806 primer regions. Should help things move a bit faster.
Decided to install QIIME2 conda environment on Mox to see if we can speed the pipeline up.
- Ran a job on Mox with the reduced 138.99 515-806 primer regions to see if this would finish a bit quicker… Still running many hours later…

20221025

Ran Linda Rhodes’ 16s pipeline with the “default” 138.99 refseqs/taxonomy. Still running…

20221024

Lab meeting
Oyster gene expression meeting (had to leave early due to contractors showing up)
Re-ran Linda Rhodes 16s pipeline with “new” MiSeq data.
- Used her original SILVA refseq and taxonomy files.
- Took hours to run on my laptop.
- Success!! Taxa barplot actually has a majority of reads in each of the samples assigned to Bacteria!!
- Will now test the SILVA 138.99 refseq and taxonomy files that I generated (followed the QIIME2 guide).
- Created a GitHub repo for storing/updating various files/notebooks associated with this project.

20221021

Dungeness crab genome annotation meeting with NOAA people (Krista, Laura, Mac).
Met with Linda to discuss weird results.
- She’s retiring at the end of the month, but will continue working on personal computer.
- She will provide data known to have generated classifications using the pipeline.
- She’ll send me here GitHub username so I can establish a repo to simplify data sharing.
- I’ll schedule recurring meetings to help keep me on task.
Lotterhos Crassostrea virginica (Eastern oyster) meeting.

20221020

Continued to work on Linda’s stuff. Tested her original ref seqs/taxonomy files, but got virtually same results as updated SILVA database/taxonomy (i.e. all samples have no assigned taxonomies)…

20221019

Began to revist Linda Rhode’s stuff after negelecting it for an entire month??!! Whoa! I literally thought it had only been a couple of weeks… Yeesh.

20221018

20221017

Read Ch. 5 of “The Disordered Cosmos”
Lab meeting - discussed Ch.5 of “The Disordered Cosmos”.
Continued the code/data migration from 2018_L18-adult-methylation repo to CEABIGR repo…

20221014

Continued the code/data migration from 2018_L18-adult-methylation repo to CEABIGR repo…

20221013

Continued the code/data migration from 2018_L18-adult-methylation repo to CEABIGR repo…

20221012

Continued the code/data migration from 2018_L18-adult-methylation repo to CEABIGR repo…
Spoke with Matt regarding RNAsequencing options/considerations for M.trossolus transcriptome.

20221011

Worked a a lot on CEABIGR data.
- Reviewing predominant isoform data, to help clarify some questions Yaamini had.
- Working on Circos plots; specifically to try to generate something “pretty” for Yaamini to use in her talk at EPIMAR tomorrow.
- Migrating, and updating, code/data from 2018_L18-adult-methylation repo to CEABIGR repo. Annoying trying to keep track of which scripts/code is in which repo…

20221006

Pub-a-thon
Continued reorganization of Circos directories within the CEABIGR repo.
Dealt with weird computer issues throughout the day (VMware Player kept freezing over and over). Potentially resolved by reducing number of CPUs that VM can use?

20221005

20221004

20221003