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:
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.
