Getting Genetics Done

Sometimes you need to run some UNIX command on a file but only want to operate on the body of the file, not the header. Create a file call...

GNU datamash is a command-line utility that offers simple calculations (e.g. count, sum, min, max, mean, stdev, string coalescing) as wel...

Software Carpentry is an international collaboration backed by Mozilla and the Sloan Foundation comprising a team of volunteers that te...

This is one of those things I picked up years ago while in graduate school that I just assumed everyone else already knew about. GNU screen ...

I've seen this question asked and partially answered all around the web. As with anything related to Perl, I'm sure there is more th...

Much of the work that bioinformaticians do is munging and wrangling around massive amounts of text. While there are some "standardized...

*Edit March 12* Be sure to look at the comments, especially the commentary on Hacker News - you can supercharge the find|xargs idea by usi...

I recently analyzed some next-generation sequencing data, and I first wanted to compare the frequencies in my samples to those in the 1000 G...

Lately I haven't written as many full length posts as usual, but here's a quick roundup of a few links I've shared on Twitter ( ...

This looks like a must-read for anyone starting out in computational biology without extensive experience at the command line.  The 135-page...

The first post on Getting Genetics Done was one year ago today. To celebrate, here are the top 10 most viewed posts since GGD launched last ...

Do you use SSH to connect to a remote Linux machine from your local Windows computer?  Ever needed to run a program on that Linux machine th...

Vanderbilt ACCRE users with PCs only... If you use ACCRE to run multi-processor jobs you'll be glad to know that they now allow you to...

In the last post I showed you how to point to a file in windows and get the full path copied to your clipboard.  I wanted to come up with s...

I tip my hat to Will for showing me this little command line trick. PLINK's output looks nice when you print it to the screen, but it c...

Ever find yourself trying to remember a series of steps you recently did in Linux? Try typing the command " history " at the comm...

I briefly mentioned "time" in the previously posted Linux command line cheat sheet , but I can't overstate its utility especia...

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 ...

And it will do way more than display "Hello, world!" to the screen. An anonymous commenter on one of our Linux posts recently ask...

`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 le...