Command line basics

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What's important versus not important

Are you a wet lab person who thinks maybe she wants to learn some informatics tools? Congratulations! Molecular biology is a quantitative science now. Trying to resist it is like a physicist resisting computers in the 1970s.

Can you do it? Of course you can. I went from pure wet lab with no computational experience whatsoever to half wet/half dry in a few years, and didn't even start until my late 30s.

The first stretch is hard - your brain will hurt - and this is because getting comfortable with the environment really is about as much work as learning a new language. It's worth it: once you get going, you'll experience a freedom to ask questions, and answer them fast, that you never thought possible. I can't overstate how much doing this has changed me as a scientist.

Below, find sections about the various things that have been useful to me. I hope they help you too.

  • Precise typing
  • Working at the command line
  • For God's sake, look at the data
  • Finding the solution all on your own
  • Using your laptop as a remote control
  • How to perform reality checks
  • Mixing and matching datasets