2021-03-23 Poinar Lab Meeting

Plague-Phylogeography Novel Synthesis and Geospatial Analysis Katherine Eaton Poinar Lab Meeting 23 March 2021 Table of Contents ...

Add outgroup to main project

Add Outgroup to Main Project

Bison Metadata for Tyler

Bison Metadata for Tyler Create [[NCBImeta Paper]] database ncbimeta/NCBImeta --config config/bison.yaml --flat ncbimeta/NCBImeta...

Calculate pPCP1 Resequencing

Calculate pPCP1 Resequencing target-coverage-perc: 80% target-coverage-bp: 7,690 bp target-depth: 100X target-bp: 6...

Change column names to lowercase

Change Column Names to Lowercase metadata.py config.py parse_tree.py clock_model.py mugration_model.py

Clade Dating Experiment

Clade Dating Experiment Problem The estimates of [[Clade clade]] [[MRCA]] are tool old. For example, [[1.ORI]]: ...

Collect results and figures

Collect Results and Figures

Construct new datasets

Construct New Datasets I've been struggling with this task for a few reasons. Alignment filtering. I can filter alignments to includ...

Create Multiple Alignments by Clade

Create Multiple Alignments by Clade Tasks Clades [[0.ANT]] [[0.PE]] [[0.PRE]] [[1.ANT]] [[1.IN]] [[1.ORI]] [[1.PRE]] ...

Create new directories for snippy and iqtree

Create New Directories for Snippy and IQTREE I want to have better organization of the output folders once filtering occurs. This will l...

Create Prune Tree and Alignment

Create Prune Tree and Alignment Prune Prune IQTREE and Alignment, No Outgroup snakemake iqtree_filter_prune_all -np --profile ...

Create a placement dataset

Create a Placement Dataset I should create a placement dataset that helps do more refined testing. 1 sample from each minor branch (N=26...

Email BEAST Log to Emil

Email BEAST Log to Emil Tasks task from "tasks" where contains(file.name, "Email BEAST Log to Emil") Email Hi Emil, I have my ...

Email Sam About BEAST

Email Sam About BEAST Tasks task from "tasks" where contains(file.name, "Email Sam About BEAST")

Evaluate singleton sites

Evaluate Singleton Sites Literature In the context of multiple sequence alignment and phylogeny reconstruction, singleton are sites ...

Execute Snakemake Rule Without Upstream

Execute Snakemake Rule Without Upstream Problem I am analyzing [[Plague Phylodynamics and Phylogeography]] on multiple c...

Extract SVG Using Puppeteer

Extract SVG Using Puppeteer Workflow The full workflow is documented in this comment. Notes Install google-chrome for WSL2 wg...

File taxes

File Taxes

Fix france being in australia

Fix France Being in Australia There is a problem in mapping

Fix Obsidian Page Build Submodule

Fix Obsidian Page Build Submodule

Integrate plague-phylogeography-paper as Submodule

Integrate plague-phylogeography-paper as Submodule Tasks Add submodule cd phd/ git submodule add https://github.com/ktmeaton/plagu...

Lab Meeting 2021-04-20

Lab Meeting 2021-04-20 Meeting Link Meeting Notes Updates There may be a vaccination plan to get students to return to campus. [...

Learn dataview

Learn Dataview File Information table file, tags from "" where file.name="Yersinia pestis" Backlinks in a file table tags from [[Yer...

Meet with ravneet

Meet With Ravneet Mention the keep-singletons filtering script change. [[Calculate Chromosome Resequencing]] [[Calculate Bait Con...

Meet with Hendrik

Meet with Hendrik [[2021-05-04]] Meeting Link Notes Present the working draft Nextstrain Narrative. Paper Objectives: ...

Plot Tip Uncertainty for 1.PRE

Plot Tip Uncertainty for 1.PRE

Read global tuberculosis paper

Read Global Tuberculosis Paper [[Zimpel 2020 Global Distribution Evolution]]

Remove the us lab strain

Remove the US Lab Strain

Review Kalamazoo Schedule

Review Kalamazoo Schedule

Run TreeTime Mugration

Run TreeTime Mugration Tasks task from "tasks" where contains(file.name, "Run TreeTime Mugration") Manual Copy Data # Tree cp /mnt/c/...

Send IBD Plots

Send IBD Plots repo commit https://github.com/ktmeaton/plague-phylogeography-projects 7...

Send Starting Tree to Australia

Send Starting Tree to Australia Tasks Send them a IQTREE that's in genetic distance (reduced, unrooted)

Separate Obsidian Repositories

Separate Obsidian Repositories Rename [[obsidian-vaults]] to [[obsidian-public]]. Create a new repository [[obsidian-private]]. R...

Stabilize Pipeline CI

Stabilize Pipeline CI

Test compute canada

Test Compute Canada Install ssh keaton@graham.computecanada.ca cd /scratch/keaton Conda Environment mamba env up...

Test Multiple MCMC Chains

Test Multiple MCMC Chains Tasks task from "tasks" where contains(file.name, "Test Multiple MCMC Chains")

Test outgroup pseudotuberculosis

Test Outgroup Pseudotuberculosis Strain Accession Status NCTC10275 SAMEA4442458 ...

Test polytomy option of iqtree

Test Polytomy Option of IQTREE

Test mvp CSS with notenote.link

Test mvp CSS with notenote.link

Update Auspice Metadata

Update Auspice Metadata Catch where province doesn't exist and coordinates are bad. Add Lat and Lon as continuous variables. Give...

Verify dates

Verify Dates seq_name date_width date_central 1/precision SAMN00715800_[671:669]_...

notenote.link

notenote.link Notes [[Markdown]] files with no [[YAML]] frontmatter don't get built into [[HTML]]. Install Create a Fork of Ma...