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Using samtools

This is my own exploration of samtools behavior and snippets of code I use in my own analyses.

The data

I am using the GRCh38 human reference from December, 2013.

There are two focal datasets of reads:

# The catalytic converter theft chain
Just had the second attempted theft of our catalytic converter. Here is a bit about context.
## Theft and fencing
I am not sure at what point the contraband enters the legitimate supply chain.
caseywdunn /
Last active May 21, 2018 17:27
Postdoc position: HIV phylogenetics in the Dunn Lab at Yale University

Working with Conda

First, some nomenclature (see 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 /
Last active September 25, 2017 18:22
Regular expressions intro and examples
caseywdunn /
Last active March 5, 2018 22:36
Notes to accompany my talk.

Evolution 2017

June 25, 2017 (and updated since then)

Casey Dunn, , @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.