davfre

SAM and BAM filtering one-liners

@author: David Fredman, david.fredmanAAAAAA@gmail.com (sans poly-A tail)
@dependencies: http://sourceforge.net/projects/bamtools/ and http://samtools.sourceforge.net/

Please extend with additional/faster/better solutions via a pull request!

BWA mapping (using piping for minimal disk I/O)

MichaelMartinez

Mac Setup and play

Lib's and Development stuff to set up

The List of Items the VM has!

1. Command Line Tools from Apple - Installed
2. Sublime Text 2 - subl has been symlink and works
3. Git use systems; can update using brew if needed in subsequent clones
4. Homebrew - Watch the changes - raring to brew
5. iTerm2 / oh-my-zsh - Need to test the plugins

yannabraham

## reproduce the figures from http://www.jstatsoft.org/v28/c01/paper using ggplot2

library(ggplot2)

## parameters
set.seed(2710)

## Figure 1
d <- rnorm(50)

simme

# First install tmux
brew install tmux

# For mouse support (for switching panes and windows)
# Only needed if you are using Terminal.app (iTerm has mouse support)
Install http://www.culater.net/software/SIMBL/SIMBL.php
Then install https://bitheap.org/mouseterm/

# More on mouse support http://floriancrouzat.net/2010/07/run-tmux-with-mouse-support-in-mac-os-x-terminal-app/