Introduction to UNIX and RNA-seq Repositories

Day 1 of the workshop. June 1st, 2026.

The slides are in Slides/ (PDF and PPTX). Answer keys for each exercise are in Exercises/answers/. Data files used in the exercises are in Exercises/data/.

Before the session

You need a terminal.

• Mac: just open Terminal.
• Linux: same, open your terminal.
• Windows: install WSL Ubuntu and open it. From PowerShell:

wsl --install -d Ubuntu
wsl -l -v
wsl -d Ubuntu

Then run the setup script from the repo:

bash setup.sh

That installs wget, sra-toolkit, and the small text utilities we use (awk, grep, sed, tar, gzip, curl). It creates ~/workshop/data and prints a check at the end. Safe to re-run.

If it fails on your machine, do not panic. Come a few minutes early and we will sort it out.

Outline

1. Setup and troubleshooting.
2. UNIX basics: navigation, inspection, pipes and redirects, text search.
3. GEO basics: accession types (GSE, GSM, SRR), common files, downloading with wget and fastq-dump.

Exercises

• Exercises/answers/Exercise1_unix.sh — directory tree, file creation, seq, mv, concatenation.
• Exercises/answers/Exercise_grep.sh — grep on happiness.csv: plain match, -w, -v, -n.
• Exercises/answers/Exercise_wordle.sh — mini-capstone: solve today's Wordle with cat | tr | egrep over /usr/share/dict/words.
• Exercises/answers/Exercise_awk_fastq.sh — awk on the paired-end FASTQ subset: read count, average length, GC%, N filtering, top 5' hexamers.
• Exercises/answers/Exercise2_geo_download.sh — wget for a GEO supplementary file and an ENA FASTQ, then fastq-dump -X 10000 for a capped SRA pull.
• Exercises/answers/Exercise3_1_counts_csv.sh — inspecting the gzipped count matrix from GSE251845.
• Exercises/answers/Exercise3_2_fastq.sh — counting reads, hexamer bias, motif search, and safely subsetting a FASTQ.

The demo accession is SRR390728 (small, public, finishes fast). The count matrix is from GSE251845.

References

• Count matrix: GSE251845.
• Paired-end FASTQ subsets: statOmics SGA2019 airway data.