Skip to content

Module 12 — Local Env + Tiny QC

Time: 60–75 min
Goal: Create a clean Conda/Mamba env and run seqtk, fastqc, and multiqc locally.

Type it, don't paste it

Muscle memory now = speed later. Please type once before copy/paste.

1) Install Miniforge

Bioinformatics often requires many specialized tools, and managing their dependencies can be tricky. Conda and Mamba create isolated environments that prevent conflicts and make analyses reproducible. Miniforge provides both commands and is the maintained conda-forge installer.

cd ~
wget -O Miniforge3.sh https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
bash Miniforge3.sh -b -p "$HOME/miniforge3"
source "$HOME/miniforge3/etc/profile.d/conda.sh"
conda init bash
conda config --set auto_activate_base false

cd ~
curl -L https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-arm64.sh -o Miniforge3.sh
file Miniforge3.sh
bash Miniforge3.sh -b -p "$HOME/miniforge3"
source "$HOME/miniforge3/etc/profile.d/conda.sh"
conda init zsh
conda config --set auto_activate_base false

cd ~
curl -L https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-x86_64.sh -o Miniforge3.sh
file Miniforge3.sh
bash Miniforge3.sh -b -p "$HOME/miniforge3"
source "$HOME/miniforge3/etc/profile.d/conda.sh"
conda init zsh
conda config --set auto_activate_base false

2) Make the env

conda create -y -n rnaseq101 -c conda-forge -c bioconda fastqc multiqc seqtk
conda activate rnaseq101

3) Prepare a tiny FASTQ and downsample

mkdir -p ~/bioinfo-course/module12 && cd ~/bioinfo-course/module12
cat > toy.fq << 'EOF'
@r1
ACGTTGCA
+
IIIIHHHF
@r2
GGGTTTAA
+
FFFFFIII
@r3
ACGTACGT
+
IIIIIIII
EOF

# Downsample "reads" (works better on real data but fine for demo)
seqtk sample -s 1 toy.fq 1.0 > toy.sub.fq

4) Run FastQC + MultiQC

mkdir -p qc
fastqc -o qc toy.fq toy.sub.fq
multiqc -o qc qc

Open qc/multiqc_report.html locally (VS Code file explorer → click to open in your default browser).

Exit Ticket (email)

Subject: Bioinfo M12 Exit Ticket – Paste:

  • Output of conda list | grep -E 'fastqc|multiqc|seqtk'
  • Two bullets from your MultiQC report (e.g., per-base quality and GC content).

Next: Module 13 — Pull One Single-Cell FASTQ