How often have you needed to extract a certain column from a file, or strip out only a few individuals from a ped file? This is often done with Excel, but that requires loading the data, manipulating it, then saving it back into a format that is acceptable, which may require converting tabs to spaces or other aggravating things.

And it will do way more than display "Hello, world!" to the screen. An anonymous commenter on one of our Linux posts recently asked how to write scripts that will automate the same analysis on multiple files. While there are potentially several ways to do this, perl will almost always get the job done. Here I'll pose a situation you may run into where perl may help, and we'll break down what this simple perl script does, line by line.

`screen` is one of the most useful system tools I've ever used. It allows you to begin a process and then detach from the process to let it continue to run in the background. You can later re-attach to the screen to check progress, even from a remote location.

For those of you who attend our computational genetics journal club every other week, you've all heard about this. Say what you will about the "consumer genetics" enterprise, 23andMe maintains an excellent blog. In their "SNPwatch" category, The Spittoon surveys and summarizes the latest findings in human genetics research before they hit the press.

If you've ever had trouble getting started doing a data analysis, you are certainly not alone. Should I run an ANOVA, MANOVA, ANCOVA, or MANCOVA? Should that have been a McNemar's test, a Kruskal-Wallis, or a Mann-Whitney U? To at least pin down the statistical test you should run, consult these excellent flowcharts by Marylyn Ritchie, Jason Moore, and Tricia Thornton-Wells.

Many of you have used this before, but for those who haven't, SNPper is a convenient little web application for quickly annotating results. So you've done your association analysis and have a list of rs-numbers you'd like to quickly get more information about.

Last week I posted a one-page reference guide that gives a short description of the Linux commands I most commonly use. To accompany this, here is a detailed walkthrough filled with examples that will introduce any beginner to the basics of using Linux in just a few hours. Many thanks to Eric Torstenson in the Ritchie lab for putting this together.

Whenever we have new students rotating through our lab who've never used Linux I always end up scrounging around the world wide series-of-tubes only to find some command line reference that's not really useful for students. So I made my own one-page reference guide that gives a basic description of most of the commands most of you will use. Feel free to distribute.

As Stephen nicely posted earlier, RSS feeds are a very powerful way to keep up with the literature -- they "push" the information to you. In addition to subscribing to individual journals, you can subscribe to a PubMed search! This will let you keep up with ALL PubMed indexed journals. To subscribe to a PubMed search, first go to www.pubmed.org and enter your search terms.

RSS rocks. In addition to consolidating all the news you read on a single page, it's also handy for keeping up with the latest publications in your favorite journals without ever going to PubMed. If you're not using RSS, give it a shot and you'll never look back. RSS stands for Really Simple Syndication.

Welcome! You've reached the first official post of Getting Genetics Done. The idea for this blog was a spin off of the short courses and workshops that Vanderbilt's Computational Genomics Core has recently been offering. Our goal for writing this is to share anything we use or hear of that makes life easier in genetics research, or boosts productivity throughout the workday in general.