The DOTSeq project: precomputed datasets

This archive contains the precomputed datasets used in the DOTSeq manuscript (Lim CS, Chieng GSW., 2026, BioRxiv, https://doi.org/10.1101/2025.09.24.678201). These datasets can be optionally used as inputs for the scripts in the DOTSeq_paper_2026 GitHub repository to reproduce the results quickly by skipping computationally intensive steps. Detailed instructions and scripts for reproducing the analyses and figures are available in the repository, which utilise DOTSeq within the Bioconductor ecosystem. Contents: Bulk Ribo-seq analysis 12 alignment files generated using STAR (*_Aligned.sortedByCoord.out.bam). 12 filtered alignment files (exonic reads) generated using DOTSeq::getExonicReads (*_Aligned.sortedByCoord.out.exonic.sorted.bam). 1 ORF read count file generated using DOTSeq::countReads (bulk.rds). Single-cell Ribo-seq analysis 27 alignment files generated using STAR (*_Aligned.sortedByCoord.out_CB.bam). 27 ORF read count files generated using DOTSeq::countReadsSingleCell (*_Aligned.sortedByCoord.out_CB.mat.rds). Metadata required for the analyses are available in the GitHub repository under the ref/ directory. Raw sequencing reads for the bulk analysis can be obtained using the sra_download.sh script.