Simulated data used in "AIDE: annotation-assisted isoform discovery with high precision" (Q10960)

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 sortedreads 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 onesynthetic annotation file (in aGTF.zip) and one bam file (e.g., sample1.sorted.bam).