Bioinformatics for Beginners – Bash

If you would like to do serious bioinformatics work, sooner or later you”re going to end up working in a Linux/Unix environment. For those of you who have no experience with bash/shell scripting, here are few links, you should check out:

If you”ve never worked in a Linux terminal before, you might want to get familiar with basic Unix commands before getting into bash scripts. Here are a few pointers to get started:

  • Linux command lists/cheat sheet: 1, 2, 3
  • A few of the most useful text manipulation tools:
    • “sed” tutorials: 1, 2
    • “grep” tutorials: 1, 2, 3, 4, 5
    • “awk” tutorials: 1, 2, 3

In general, there are a few things you should keep in mind:

  • Don”t panic! You might not get everything right on the first try, but eventually you will.
  • If you get stuck, google! Most common problems have a solution (or more frequently several solutions) available online. (Make sure to at least try to understand the code you found online!)
  • Always test your code/command with a small (and preferably representative) subset of your sample/input file!
  • Try to practice as much as you can!
    • You can revisit and improve your old scripts.
    • You can try to create multiple solutions for a problem (e.g. with sed and awk).
    • Write small scripts/programmes that could be useful for  your work or everyday tasks!
    • Participate in online challenges (e.g. check out the Euler Project, the Python Challenge, beginner challenges on Ubuntu Forums, Stack Overflow challenges)!
    • Help others with their problems! There are several forums around, where people ask for help with scripting/programming problems. Providing an answer or solution for someone”s problem is great practice. Plus, you”ll most likely get some feedback and tips from other, more experienced forum members as well.