RNA-seq Analysis: Reads to Differential Expression
Workflow Overview
FASTQ → QC (FastQC/fastp) → Alignment (STAR/HISAT2) → Counting (featureCounts)
→ Pseudo-align (Salmon/kallisto) → tximport
→ Count matrix → Normalization → DESeq2/edgeR → GSEA
Experimental Design Rules
- Replicates: ≥3 biological replicates per condition; more replicates > deeper sequencing
- Depth: 10–30M reads for gene-level DE; 50–100M for isofor
[Description truncada. Veja o README completo no GitHub.]