Agricultural Statistics & Bioinformatics Insights

Quality Control: Assess raw read quality using FastQC and perform trimming/filtering if needed
Read Alignment: Map reads to reference genome using aligners like STAR or HISAT2
Quantification: Generate count matrices using featureCounts or HTSeq
Normalization: Apply appropriate normalization (e.g., TMM for edgeR, median‑of‑ratios for DESeq2)
Differential Expression: Identify significantly differentially expressed genes
Functional Analysis: Perform gene ontology enrichment and pathway analysis

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