This is my own exploration of samtools behavior and snippets of code I use in my own analyses.
I am using the GRCh38 human reference from December, 2013.
There are two focal datasets of reads:
- Nanomia, NA19 V3698-D2. SRR23143273
Casey Dunn caseywdunn
caseywdunn
/ using_samtools.md
Last active
August 8, 2023 19:41
caseywdunn
/ 2023_invertomics.md
Created
March 23, 2023 10:12
Some links...
Phylogenetic Biology, a book
caseywdunn
/ rust.md
Last active
February 1, 2023 22:55
Some notes as I learn Rust.
caseywdunn
/ catalytic
Created
November 30, 2021 18:21
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| # The catalytic converter theft chain | |
| Just had the second attempted theft of our catalytic converter. Here is a bit about context. | |
| ## Theft and fencing | |
| https://youtu.be/ZGLrRj7AJsc?t=172 | |
| I am not sure at what point the contraband enters the legitimate supply chain. |
caseywdunn
/ data_visualization_class.md
Last active
April 5, 2021 18:29
Some basic notes for a couple hour discussion about data visualization.
Build on a few points from my previous course.
To read in advance of the class: https://r4ds.had.co.nz/data-visualisation.html .
caseywdunn
/ harvard2019.md
Last active
May 10, 2019 11:10
Short url: https://git.io/fjchB
10 May 2019
caseywdunn
/ postdoc_dunnlab_2018.md
Last active
May 21, 2018 17:27
Postdoc position: HIV phylogenetics in the Dunn Lab at Yale University
Please share this link to the ad: https://git.io/yale_postdoc_2018
Advisor: Casey Dunn
Location: Department of Ecology and Evolutionary Biology, Yale University, in New Haven, Connecticut, USA
Application due date: June 1, 2018 (or until filled)
caseywdunn
/ conda.md
Last active
January 7, 2018 00:19
First, some nomenclature (see https://conda.io/docs/glossary.html for more):
- A recipe is a flat directory that has the information needed to build a package
- A package is a "compressed file that contains everything that a software program needs in order to be installed and run... You manage conda packages with conda."
- An environment is a "directory that contains a specific collection of conda packages and their dependencies, so they can be maintained and run separately without interference from each other."
A typical workflow:
caseywdunn
/ PCfB_Regular_Expressions.md
Last active
September 25, 2017 18:22
Regular expressions intro and examples
These examples of regular expressions are taken largely from our book Practical computing for Biologists. More information is available at http://practicalcomputing.org.
This document can be accessed via the delightful github url shortener at https://git.io/dine
Given the following names:
Agalma elegans
Frillagalma vitiazi
June 25, 2017 (and updated since then)
Casey Dunn, http://dunnlab.org , @caseywdunn
These are some notes and annotated references relevant to my talk with Stacey Smith in the symposium "SSB Symposium Phylogenetic approaches to connecting genotypes to phenotypes" at Evolution 2017.
If you are interested in any of this work let me know. I am moving to Yale and looking for people to join the new research group.
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