Week 4: Working with files in the Unix shell
Overview
This week, we will focus on working with files in the Unix shell. Because we’re going to start working with (DNA/RNA/protein) sequence files, you’ll also get introduced to various genomics file types. Finally, you’ll learn about the specific files from the example dataset you’ll work with throughout the course.
Learning goals & lectures
A) Genomics file types and the example dataset (Monday)
- What genomics file types like FASTA, FASTQ, and GFF/GTF are for, and what they look like.
- How base-call quality scores are coded in FASTQ files.
- What the experimental design is for the course’s example dataset.
- Which files are in our example dataset.
B) Working with files in the Unix shell I: The shell as a file browser (Monday/Wednesday)
Learn to use Unix shell commands to:
- Create, copy, move, rename, and delete directories and files
- Select multiple files with globbing
C) Working with files in the Unix shell II: Viewing, summarizing, and manipulating files (Wednesday)
Learn to use Unix shell commands to:
- View the contents of text files in various ways
- Use redirection and the pipe to flexibly process the output of commands
- Search within, manipulate, and extract information from text files
Assignments & exercises
- Week 4 exercises
- No assignments this week
Readings
- Garrigós et al. (2025): “Two avian Plasmodium species trigger different transcriptional responses on their vector Culex pipiens”
This is the paper associated with the dataset we will use throughout the course, starting this week. - Lecture C has a self-study section at the end. (This note was added on 2023-09-15)
Optional self-study material
- Buffalo (2015) — Chapter 3: “Remedial Unix Shell” and Chapter 7: “Unix Data Tools” (OSU library link )
References
Buffalo, Vince. 2015. Bioinformatics Data Skills [Reproducible and Robust Research With Open Source Tools]. First edition. O’Reilly.
Garrigós, Marta, Guillem Ylla, Josué Martínez-de la Puente, Jordi Figuerola, and María José Ruiz-López. 2025. “Two Avian Plasmodium Species Trigger Different Transcriptional Responses on Their Vector Culex pipiens.” Molecular Ecology 34 (15): e17240. https://doi.org/10.1111/mec.17240.