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 called body somewhere in your $PATH, make it executable, and add this to it: #!/bin/bash IFS= read -r header printf '%s\n' "$header" eval $@ Now, when you need to run something but ignore the header, use the body command first.

GNU datamash is a command-line utility that offers simple calculations (e.g. count, sum, min, max, mean, stdev, string coalescing) as well as a rich set of statistical functions, to quickly assess information in textual input files or from a UNIX pipe.

Software Carpentry is an international collaboration backed by Mozilla and the Sloan Foundation comprising a team of volunteers that teach computational competence and basic programming skills to scientists.

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 is a great utility built-in to most Linux installations for remote session management. Typing 'screen' at the command line enters a new screen session.

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 than one way to do it. Here's how I do it with Perl 5.10.1 on CentOS 6.4. First, install local::lib with bootstrapping method as described here.

Much of the work that bioinformaticians do is munging and wrangling around massive amounts of text. While there are some "standardized" file formats (FASTQ, SAM, VCF, etc.) and some tools for manipulating them (fastx toolkit, samtools, vcftools, etc.), there are still times where knowing a little bit of Unix/Linux is extremely helpful, namely awk, sed, cut, grep, GNU parallel, and others.

*Edit March 12* Be sure to look at the comments, especially the commentary on Hacker News - you can supercharge the find|xargs idea by using find|parallel instead. --- Do you ever discover a trick to do something better, faster, or easier, and wish you could reclaim all the wasted time and effort before your discovery?

I recently analyzed some next-generation sequencing data, and I first wanted to compare the frequencies in my samples to those in the 1000 Genomes Project. It turns out this is much easier that I thought, as long as you're a little comfortable with the Linux command line. First, you'll need a Linux system, and two utilities: tabix and vcftools. I'm virtualizing an Ubuntu Linux system in Virtualbox on my Windows 7 machine.

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 (@genetics_blog) over the last week: First, 23andMe is having a big DNA Day Sale ($108) for the kit + 1 year of their personal genome subscription service https://www.23andme.com/. Previously mentioned R IDE RStudio released a new beta (version 0.93) that includes several new features and bugfixes.

This looks like a must-read for anyone starting out in computational biology without extensive experience at the command line.  The 135-page document linked at the bottom of the Google Group page looks like an excellent primer with lots of examples that could probably be completed in a day or two, and provides a great start for working in a Linux/Unix environment and programming with Perl.