This repository contains the eight simulated RNA-seq samples (sample1, sample2, ..., sample8 with coverages10x, 20x, ..., 80x) simulated from the annotation file "truth.gtf" by R package polyester. The simulation procedure is described in the Methods section "Simulation for comparing isoform reconstruction methods". For example, sample 1 has mapped and sorted reads in "sample1.sorted.bam". When we generate the benchmarking results in the Results section "AIDE outperforms state-of-the-art methods on simulated data", we supply each isoform identification/quantification method (AIDE, Cufflinks, StringTie, or SLIDE) with one synthetic annotation file (in "aGTF.zip") and one bam file (e.g., sample1.sorted.bam).

{"references": ["Li, Wei Vivian, Shan Li, Xin Tong, Ling Deng, Hubing Shi, and Jingyi Jessica Li. \"AIDE: annotation-assisted isoform discovery with high precision.\" Genome research 29, no. 12 (2019): 2056-2072."]}