Category: BINF 2111

BINF 2111: Know your UNIX, part 2 (Homework)

BINF 2111: Know your UNIX, part 2 (Homework)

For your homework (due next Thursday), I want you to go all the way to the end of the book to Chapter 16 and learn the following commands. I mentioned “cut” and “paste” in class...

BINF 2111: Variables and conditionals in bash

BINF 2111: Variables and conditionals in bash

A good script should be: Reusable Efficient Clearly organized Correct in how it performs its task Error-/bug-free Today you’re going to learn two key elements of bash scripting:  use of variables, and use of...

BINF 2111: Assembly at the Command Line (Lab)

BINF 2111: Assembly at the Command Line (Lab)

Today’s lab task is preparation for developing a script that will assemble a batch of small genome sequence data sets. In our script development process there are four main steps: Figure out the pipeline...

BINF 2111: Know your UNIX, part 1

BINF 2111: Know your UNIX, part 1

Before we move on to scripting, we’ve got to get a handle on the basic UNIX commands covered in Chapters 4 and 5 of the book. You can’t write a script until you understand...

BINF 2111: Know your UNIX (part 3)

BINF 2111: Know your UNIX (part 3)

The homework for next week (due next Tuesday) is an opportunity to practice writing a few small scripts. Work through the exercises on p. 88-98 of your book. You will practice making scripts executable using...

BINF 2111: Assembly at the command line

BINF 2111: Assembly at the command line

The most common things that you’ll want to do with shell scripts in bioinformatics are 1) data manipulation and 2) driving programs to run automatically, collecting their output, and feeding it into other programs....