Fig. 1

Workflow diagram of the RNA-seq analysis. Overview of the data analysis pipeline. The pipeline begins with the acquisition of raw reads in FASTQ format. These reads are then assessed for quality using the FastQC program. Terminal low-quality bases and adapter sequences are subsequently trimmed off. Mapped files in BAM format are then generated from the processed reads and raw read counts are quantified. The pipeline proceeds with differential gene expression analysis. The resulting differentially expressed genes (DEGs) are analysed for Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment. Starting from BAM input files, the pipeline also includes a parallel branch analysis for identifying Differential Alternative Spliced Genes (DAS), enriched by a splicing events distribution analysis and a GO- and KEGG- enrichment analysis for DAS. Finally, miRNA analysis is conducted as part of the small-RNA seq process. This comprehensive pipeline provides a robust approach to RNA-Seq data analysis, from raw reads to functional insights..