Simulated data used in "AIDE: annotation-assisted isoform discovery with high precision"
DOI10.5281/zenodo.6522761Zenodo6522761MaRDI QIDQ6680195FDOQ6680195
Dataset published at Zenodo repository.
Jingyi Jessica Li, Wei Vivian Li
Publication date: 5 May 2022
Copyright license: Creative Commons Attribution 4.0 International
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).
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