STAGE 01 · Quality Control · tools: FastQC · MultiQC · NanoStat
Per-base PHRED quality score distribution
5' end · Q40+ position → 3' end · Q20
metric sample_01 status
total_reads 2.4M PASS
mean_quality Q38.4 PASS
N50_read_len 18.4 kb PASS
adapter_content 2.3% PASS
STAGE 02 · Alignment · tools: minimap2 · STAR · samtools
Genome browser - chr1:1,234,500–1,235,200 · TERA-Seq
98.4% reads aligned ·
1.6% unmapped ·
0.2% multi-map
STAGE 03 · Quantification · tools: featureCounts · HTSeq · Salmon
Count matrix excerpt - TPM-normalized
gene_id ctrl_1 ctrl_2 trt_1 trt_2
ENSG00000001 142.3 138.7 421.8 398.2
ENSG00000002 88.1 91.4 22.4 19.8
ENSG00000003 301.2 288.9 296.1 310.4
... 18,342 more
STAGE 04 · Differential Expression · tools: DESeq2 · edgeR
Volcano plot - treatment vs control (FDR < 0.05, |log2FC| > 1)
log2FoldChange
−log10(padj)
up (847)
down (623)
STAGE 05 · Pathway Enrichment · tools: fgsea · clusterProfiler
Top enriched pathways - NES score (FDR < 0.25)
APOPTOSIS_REGULATION
−1.84
STAGE 07 · Report & Repository · deliverables: GitHub + PDF
project_OE-2025-001/
├── Snakefile
├── config/
└── config.yaml
├── workflow/
├── qc.smk
├── align.smk
└── deseq2.smk
├── results/
├── figures/ (PDF + PNG)
├── deseq2_results.tsv
└── interpretation_report.pdf
└── README.md