Illumina just unveiled their latest sequencing machine, the HiSeq 2000, capable of sequencing two human genomes to 30x coverage in a single run for less than $10,000 each. Using reversible terminator-based sequencing by synthesis chemistry, the HiSeq 2000 is capable of quickly generating a flood of data: 200 Gb per run, 2 x 100 bp read length, up to 25 Gb per day, two billion paired-end reads/run.
This looks good. 208 Light Hall Wednesday 1/13/2010, Noon Charles Rotimi Health Disparities in the Genomic Era: What are we Learning? Charles Rotimi, PhD, a genetic epidemiologist and a biochemist, is a senior investigator in the Inherited Disease Branch of the NHGRI intramural program.
It took several months after learning about ggplot2 before I gave it a try myself. I was apprehensive about learning a new graphics system with a new set of commands. Thing is, if you've ever used plot() in R, you already know how to use much of the functionality in ggplot2! In this tutorial I want to show you just how easy it is to start producing high-quality graphics using ggplot2.
The Vanderbilt Genome Technology Core is hosting a seminar/workshop on next-generation sequencing where Vanderbilt investigators will share their experiences with several types of next-gen technologies. You can visit the Genome Technology Core at
Ben's paper was published today in the 2010 proceedings of the Pacific Symposium in Biocomputing. You can download the PDF here.
The 2010 Cancer Biostatistics Workshop seminar series begins next Friday with a workshop by Ayumi Shintani on sample size estimation and power analysis. Here's the entire 2010 workshop schedule. Be sure to check out my previous post on software for power calculations in genetic analysis.
Learning R blog details some of the new features in the latest update to ggplot2. The latest version includes functions to make it easier to change axis and legend labels, as well as a function to easily set the limits of the plot display outside the range of the data. Be sure to check back next week - I'm putting together a short introductory ggplot2 tutorial.
I've covered plyr once before, showing you how to get means and variances for two quantitative traits across multilocus genotypes. JD Long over at Cerebral Mastication recently posted a nice screencast illustrating how plyr "just works" as an alternative to R's family of apply commands.
Just discovered this very handy R command to capture the output from a system command as an R object. I wanted to use R to read in the output from another program (PLINK) and do some processing on each output file. Of course if the files are named sequentially (plink1.out, plink2.out, plink3.out, etc.) this would be simple with a for loop.
Do you ever find yourself switching back and forth between your work computer, your laptop, and your home computer? This happens to me all the time when I'm writing. Rather than carry all your files on a USB stick and risk losing it or corrupting your data, give Dropbox a try. It's dead simple, and works for PC, Mac, and Linux too.
A tip of the hat to a commenter on my previous coverage of a next-gen sequencing paper for pointing out this detailed and perhaps more technically-oriented review on sequencing by synthesis recently published in Nature Biotechnology. Thanks, Clive. Review: The challenges of sequencing by synthesis (Nature Biotechnology)Getting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC BY) License.