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 year. Incidentally, nine of the ten are tutorials on how to do something in R. Thanks to all the readers and all the commenters for sharing your thoughts!
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 that displays graphical output, or uses a GUI? I was in this position last week trying to make figures using ggplot2 in R of results from an analysis of GWAS data which required using a 64-bit Linux machine with more RAM than my 32-bit windows machine can see.
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 map your home directory to your local desktop using Samba (so you can access your files through My Computer as you normally would with local files).
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 something similar for a Linux environment. This is helpful on Vampire/ACCRE because you have to fully qualify the path to every file you use when you submit jobs with PBS scripts.
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 can be a pain to load the output into excel or a MySQL database because all the fields are separated by a variable number of spaces. This little command line trick will convert a variable-space delimited PLINK output file to a comma delimited file.You need to be on a Linux/Unix machine to do this.
Ever find yourself trying to remember a series of steps you recently did in Linux? Try typing the command "history" at the command line (without the quotes). You'll see a long list of your most recently used commands.
I briefly mentioned "time" in the previously posted Linux command line cheat sheet, but I can't overstate its utility especially for ACCRE/Vampire users. The time command does exactly what it sounds like: it times exactly how long it takes to run anything at the command line. And it couldn't be easier to use.
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.
`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.