--- author: Sam White toc-title: Contents toc-depth: 5 toc-location: left layout: post title: Daily Bits - October 2022 date: '2022-10-01 10:37' tags: - daily bits categories: - 2022 - Daily Bits --- 20221031 - Lab meeting. - Discussed Ch.6 of "The Disordered Cosmos". - Worked on CEABIGR manuscript in preparation for Friday's meeting with Kaite Lotterhos. --- 20221028 - Science Hour - Worked heavily on getting CEABIGR max transcript counts Circos formatting. --- 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). --- 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)](https://en.wikipedia.org/wiki/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 - Took day off --- 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](https://github.com/epigeneticstoocean/2018_L18-adult-methylation) to CEABIGR repo... --- 20221014 - Continued the code/data migration from [2018_L18-adult-methylation repo](https://github.com/epigeneticstoocean/2018_L18-adult-methylation) to CEABIGR repo... --- 20221013 - Continued the code/data migration from [2018_L18-adult-methylation repo](https://github.com/epigeneticstoocean/2018_L18-adult-methylation) to CEABIGR repo... 20221012 - Continued the code/data migration from [2018_L18-adult-methylation repo](https://github.com/epigeneticstoocean/2018_L18-adult-methylation) 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](https://github.com/epigeneticstoocean/2018_L18-adult-methylation) 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 - Lab cleanup extravaganza - Installed 2nd gas cylinder bracket in FTR 213 - Cleaned up my computer area. - Cleaned up my old office. - Moved Brent's stuff to FTR 228. - Moved Friedman qPCR machine to FTR 228. - Helped "clean" up MAR cold room (watched Steven sweep). --- 20221004 - Lab cleanup extravaganza - Cleaned out 213 4oC fridge - Restored T21 table top centrifuge sign up sheet - Moved NOAA/Jensen crab bins to FTR 228 - Evaluated middle freezer in -80oC room - Fixed FRT 209 printer (ethernet connection had to be enabled in printer settings, despite cable being plugged in). - Cleaned my bench. --- 20221003 - Day off