Simulated arabidopsis long read RNA-seq

Simulated arabidopsis long RNA-seq data used for benchmarking isoform identification and quantification as part of the paper: "Accurate strand-specific de novo long-read transcript isoform discovery and quantification at bulk, single-cell, and single-nucleus resolution" by Yu et al. 2026 Genome resources are as follows: See https://zenodo.org/records/20719930 for reference data. Reference GTF annotations: Araport11_GTF_genes_transposons.May2023.pigeon2_cleaned_with_gene.gtf : full gene set Araport11_GTF_genes_transposons.May2023.pigeon2_cleaned_with_gene_1isoformPerGene_reduced.gtf : single isoform retained per gene for use with ref-guided isoform ID experiments. Araport11_GTF_genes_transposons.May2023.pigeon2_cleaned_with_gene_expressed.gtf : expressed subset Araport11_GTF_genes_transposons.May2023.pigeon2_cleaned_with_gene_1isoformPerGene_expressed_kept.gtf : the single isoform retained among the expressed isoform subset. Quantification Truth set: Arabidopsis_transcript_id_count.tsv IsoSeqSim simulated reads aligned to the reference genome: Arabidopsis_isoseqsim_simulated_reads_gpd_start_e0000_modified_sorted_filtered.bam : sequence error-free Arabidopsis_isoseqsim_simulated_reads_gpd_start_e0016_modified_sorted_filtered.bam : 1.6% seq error Arabidopsis_isoseqsim_simulated_reads_gpd_start_e0050_modified_sorted_filtered.bam : 5% seq error Arabidopsis_isoseqsim_simulated_reads_gpd_start_e0085_modified_sorted_filtered.bam : 8.5% seq error * updated version uses minimap2 2.30-r1287 for improved alignments.