Resources & Practice
A practical path: pick one dataset, run an end-to-end workflow, write down every assumption, and produce a short report with plots. Repetition builds intuition.
Suggested practice exercises
- QC: Run FastQC/MultiQC and explain 5 plots in your own words.
- Trimming: Compare before/after read length and adapter metrics.
- Alignment: Produce mapping %, duplicate %, insert size; explain changes across samples.
- Variants: Filter a VCF; justify thresholds using depth/MAPQ/strand bias metrics.
- RNA-seq: Create a volcano plot and interpret effect size vs significance.
- Metagenomics: Show stacked taxa bars + alpha diversity; discuss compositional caveats.
A lightweight reporting template
When you finish a workflow, capture:
- Dataset source + accession (or internal ID)
- Reference build + annotation versions
- Software versions + parameters
- QC plots and pass/fail decisions
- Key results (tables + 2–4 plots)
- Limitations and next steps
Command-line mini cheat sheet
# FASTQ
zcat reads.fastq.gz | head
expr $(zcat reads.fastq.gz | wc -l) / 4
# BAM
samtools view -H sample.bam | head
samtools flagstat sample.bam
# VCF
bcftools view -h sample.vcf.gz | head
bcftools view -H sample.vcf.gz | head
More resources coming soon
Check back later for curated tool catalogs and protocols.