| Raw RNA-Seq reads were processed using Trimmomatic to remove adapters and low-quality bases, discarding reads shorter than 60 bp. High-quality reads were aligned to the Artocarpus reference genome using HISAT2. Transcript assembly and quantification were performed with StringTie, merging individual assemblies into a unified transcript set. Expression levels were normalized to TPM/FPKM using Ballgown, followed by TMM normalization to generate the final expression matrix. |
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