A refined Saccharomyces cerevisiae reference transcriptome from Direct RNA Sequencing, with a reusable pipeline for UTR annotation updates

Data and code accompanying the manuscript: A refined Saccharomyces cerevisiae reference transcriptome from Direct RNA Sequencing, with a reusable pipeline for UTR annotation updates (Rossini et al, 2026). This resource provides per-gene 5′ and 3′ UTR lengths for S. cerevisiae derived from Oxford Nanopore Direct RNA Sequencing (DRS), merged with the Nagalakshmi et al. (2008) short-read RNA-seq annotation. The merge rule guarantees that no Nagalakshmi boundary is ever shortened: at each boundary and for each gene, the longer of the two estimates is retained. Contents: Data/Annotation/ — final UTR annotation tables (TSV/CSV/GFF3) and transcript FASTA references Data/Bam/ — representative sorted, indexed BAM files for DRS and short-read alignments Data/Metrics/ — pre-computed alignment quality metrics and metagene coverage profiles scripts/ReferenceConstruction/ — R and Python scripts to reproduce the annotation pipeline (steps 1–4) scripts/Preprocessing/ — HPC shell scripts for alignment and metrics computation scripts/Figures/ — Python and R scripts to reproduce all manuscript figures Code is also available on GitHub: https://github.com/Arnaroo/Yeast_Annotation