Lesson 1 - Fundamentals and Basic Commands

Learning Objectives

• Explain why the Linux CLI is central to bioinformatics workflows.
• Navigate the filesystem with absolute and relative paths.
• Inspect files safely using less, head, and tail.
• Use core commands to copy, move, and remove files in a controlled workspace.
• Count and search within FASTQ files using wc and grep.
• Apply WSL-specific tips for file locations and performance.

Conceptual Overview

Linux is designed around small tools that do one job well and can be combined. In bioinformatics, datasets are large and automated pipelines are common, so the command line is faster, more reproducible, and often required by analysis tools.

The filesystem is a tree rooted at /. Your home directory ($HOME) is your personal workspace. Paths can be absolute (start with /) or relative (start from your current directory). In WSL, Windows drives appear under /mnt, so your Windows C: drive is /mnt/c.

WSL notes:

• Performance is usually better when you keep bioinformatics data inside the Linux filesystem (e.g., under /home/...) instead of /mnt/c.
• Windows and Linux line endings differ; most bioinformatics tools expect Linux line endings.
• Use Linux paths in commands, even when the data started on Windows.

Worked Examples

1) Where am I?

pwd prints the absolute path to your current directory.

pwd

Output:

/mnt/c/Users/WAVECU001/Documents/Bioinformatic_Fridays

2) List folders and files

ls lists the contents of a directory.

ls Training

Output:

long_reads
short_reads

ls -l uses the -l option for a long listing with permissions, size, and timestamps.

ls -l Training/short_reads/paired

Output:

total 109600
drwxrwxrwx 1 bodeoni bodeoni     4096 Jan 16 16:45 SRR1553607
-rwxrwxrwx 1 bodeoni bodeoni 56113290 Jan 16 11:34 SRR1553607_1.fastq
-rwxrwxrwx 1 bodeoni bodeoni 56113290 Jan 16 11:34 SRR1553607_2.fastq

3) Change directories with cd

cd changes your current directory. pwd confirms where you are.

cd Training/short_reads/paired
pwd

Output:

/mnt/c/Users/WAVECU001/Documents/Bioinformatic_Fridays/Training/short_reads/paired

4) Inspect FASTQ safely

head -n 8 uses the -n option to show the first 8 lines.

head -n 8 Training/short_reads/paired/SRR1553607_1.fastq

Output:

@SRR1553607.1 1 length=101
GTTAGCGTTGTTGATCGCGACGCAACAACTGGTAAAGAATCTGGAAGAAGGATATCAGTTCAAACGCTCAAGCGAGATGATGGATATTTTTGAACGACTCA
+SRR1553607.1 1 length=101
BB@FFFFFHHHHHJJJJJJJJJJJJJJJJJJJGHIJJJJJJJJJHHHHHFFFFFEEEEEEEEEDDDDDDDDDDDDDDDDDEDDDDEDEEEDDDDDDDDDDD
@SRR1553607.2 2 length=101
GGTGTAAGCACAGTACTCGGCCCACATCGCCTTTGTGTTAATGAAGTTTGGGTATCAACTTTCATCCCCAATCTTCCGTGGAAGGAGTATGTTCCGTCAAT
+SRR1553607.2 2 length=101
?@;BDDDDFHFHFFFGIIGHIIJJGJIGIJIIIIGDGGGHEIGJIIIGIIHJ5@FGHJJIEGGEEHHFFFFFFEEDEDCBB?CCDDD?CDDDDECDCB@>C

tail -n 4 uses the -n option to show the last 4 lines.

tail -n 4 Training/short_reads/paired/SRR1553607_1.fastq

Output:

@SRR1553607.203445 203445 length=101
CTCGGGTTCCGCACGGTCACCACAACCTCGTTGCCCTCGCCCGCCGCGCGGGCCCACCTGAGCTGGCTGGCCGATTTCTCCGGCCCACCTGGCAGCATGGC
+SRR1553607.203445 203445 length=101
CCCFFFDDHHDFHIJIHHGIJJJJJIJJJIIJJJIJJJGJJJGIHFCD@B@BDDDDDBDDDDDDDDDDDDDDDBDDDCEDDDBDBDDDDDDBDDDDBDCDD

5) Browse with less

less opens a scrollable viewer for large files. Press q to quit. No output appears because it is interactive.

less Training/long_reads/barcode57.fastq

6) View a small text file with cat

cat prints an entire small file to the screen.

cat Training/short_reads/unpaired/download.sh

Output:

#!/usr/bin/env bash
curl -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR112/009/SRR11282409/SRR11282409.fastq.gz -o SRR11282409_Healthy.fastq.gz
curl -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR112/007/SRR11282407/SRR11282407.fastq.gz -o SRR11282407_Case.fastq.gz
curl -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR112/008/SRR11282408/SRR11282408.fastq.gz -o SRR11282408_Healthy.fastq.gz
curl -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR112/013/SRR11282413/SRR11282413.fastq.gz -o SRR11282413_Healthy.fastq.gz
curl -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR112/012/SRR11282412/SRR11282412.fastq.gz -o SRR11282412_Case.fastq.gz
curl -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR112/010/SRR11282410/SRR11282410.fastq.gz -o SRR11282410_Case.fastq.gz
curl -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR112/011/SRR11282411/SRR11282411.fastq.gz -o SRR11282411_Healthy.fastq.gz

7) Count lines in a FASTQ

wc -l uses the -l option to count lines. FASTQ has 4 lines per read, so divide the line count by 4 to estimate reads.

wc -l Training/short_reads/paired/SRR1553607_1.fastq

Output:

813780 Training/short_reads/paired/SRR1553607_1.fastq

8) Search within a file

grep -m 2 uses the -m option to stop after 2 matches. ^@ means the line starts with @.

grep -m 2 "^@SRR1553607\." Training/short_reads/paired/SRR1553607_1.fastq

Output:

@SRR1553607.1 1 length=101
@SRR1553607.2 2 length=101

9) Safe workspace edits

mkdir -p uses the -p option to create parent folders if they do not exist. No output is expected when it succeeds.

mkdir -p Module_1_Linux/workspace

cp copies a file, and mv renames or moves a file. No output is expected when these commands succeed.

cp Training/short_reads/unpaired/download.sh Module_1_Linux/workspace/
mv Module_1_Linux/workspace/download.sh Module_1_Linux/workspace/download_script.sh

rm deletes a file permanently, so double-check the path before you run it.

rm Module_1_Linux/workspace/download_script.sh

Exercises

1. Use pwd and ls to navigate into Training/long_reads. What is the name of one FASTQ file you see there?

2. Use head -n 4 to inspect the first read in Training/long_reads/barcode57.fastq. What does the header line start with?

3. Use tail -n 4 on the same file. Compare the first and last header lines. What looks similar or different?

4. Use wc -l on Training/short_reads/paired/SRR1553607_2.fastq. Expected output: 813780 Training/short_reads/paired/SRR1553607_2.fastq.

5. Use grep -m 1 "^@" on Training/short_reads/paired/SRR1553607_2.fastq. What does the first header line look like?

6. Create a workspace inside Module_1_Linux/ and copy Training/short_reads/unpaired/download.sh into it with a new name of your choice.

7. Challenge: Use wc -l to estimate the number of reads in Training/short_reads/paired/SRR1553607_1.fastq and Training/short_reads/paired/SRR1553607_2.fastq. Are they the same?

Solutions

Solution 1

ls lists files in the directory after you change into it.

ls Training/long_reads

Output:

barcode57.fastq
barcode58.fastq
sample3.fastq

Solution 2

head -n 1 shows just the first header line.

head -n 1 Training/long_reads/barcode57.fastq

Output:

@5832c8b6-696e-46cd-be8d-73b789952b4e  st:Z:2024-06-27T02:52:17.771+00:00  RG:Z:fba2136ff67b57066e5c7e23383eba9e075ff2b2_dna_r10.4.1_e8.2_400bps_sup@v4.3.0

Solution 3

tail -n 4 shows the last read, and head -n 1 selects the header line from those 4 lines. Compare this header to the first header for differences.

tail -n 4 Training/long_reads/barcode57.fastq | head -n 1

Output:

@4492b0c6-6608-4405-a985-7b409c70ef7d  st:Z:2024-06-27T07:46:29.526+00:00  RG:Z:fba2136ff67b57066e5c7e23383eba9e075ff2b2_dna_r10.4.1_e8.2_400bps_sup@v4.3.0

Solution 4

wc -l counts lines in the file.

wc -l Training/short_reads/paired/SRR1553607_2.fastq

Output:

813780 Training/short_reads/paired/SRR1553607_2.fastq

Solution 5

grep -m 1 stops after the first match, and ^@ means the line starts with @.

grep -m 1 "^@" Training/short_reads/paired/SRR1553607_2.fastq

Output:

@SRR1553607.1 1 length=101

Solution 6

mkdir -p creates the workspace and cp copies the file into it.

mkdir -p Module_1_Linux/workspace
cp Training/short_reads/unpaired/download.sh Module_1_Linux/workspace/download_copy.sh
ls Module_1_Linux/workspace

Output:

download_copy.sh

Solution 7

wc -l counts lines; divide by 4 to estimate reads. Each file has 813780 lines, so each has 203445 reads.

wc -l Training/short_reads/paired/SRR1553607_1.fastq
wc -l Training/short_reads/paired/SRR1553607_2.fastq

Output:

813780 Training/short_reads/paired/SRR1553607_1.fastq
813780 Training/short_reads/paired/SRR1553607_2.fastq