ArticleBioinformatics (Oxford, England)2011
Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM).
Article in Bioinformatics (Oxford, England), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 202 papers.
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Who cites it
202 citing papers in PubMed.
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- BEERS2: RNA-Seq simulation through high fidelity in silico modeling.Briefings in bioinformatics · 2024Article
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- Alternative splicing of pre-mRNA modulates the immune response in Holstein cattle naturally infected withFrontiers in immunology · 2024Article
- Alternative RNA Splicing in the Retina: Insights and Perspectives.Cold Spring Harbor perspectives in medicine · 2023Review
- Hyperglucagonaemia in diabetes: altered amino acid metabolism triggers mTORC1 activation, which drives glucagon production.Diabetologia · 2023Article
- A scoping review on deep learning for next-generation RNA-Seq. data analysis.Functional & integrative genomics · 2023Article
- Temporal progress of gene expression analysis with RNA-Seq data: A review on the relationship between computational methods.Computational and structural biotechnology journal · 2023Review
- Boquila: NGS read simulator to eliminate read nucleotide bias in sequence analysis.Turkish journal of biology = Turk biyoloji dergisi · 2023Article
- The role of Meteorin-like in skeletal development and bone fracture healing.Journal of orthopaedic research : official publication of the Orthopaedic Research Society · 2022Article
- Techniques for Profiling the Cellular Immune Response and Their Implications for Interventional Oncology.Cancers · 2022Review
142 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors.
Funding
Abstract
motivationA critical task in high-throughput sequencing is aligning millions of short reads to a reference genome. Alignment is especially complicated for RNA sequencing (RNA-Seq) because of RNA splicing. A number of RNA-Seq algorithms are available, and claim to align reads with high accuracy and efficiency while detecting splice junctions. RNA-Seq data are discrete in nature; therefore, with reasonable gene models and comparative metrics RNA-Seq data can be simulated to sufficient accuracy to enable meaningful benchmarking of alignment algorithms. The exercise to rigorously compare all viable published RNA-Seq algorithms has not been performed previously.
resultsWe developed an RNA-Seq simulator that models the main impediments to RNA alignment, including alternative splicing, insertions, deletions, substitutions, sequencing errors and intron signal. We used this simulator to measure the accuracy and robustness of available algorithms at the base and junction levels. Additionally, we used reverse transcription-polymerase chain reaction (RT-PCR) and Sanger sequencing to validate the ability of the algorithms to detect novel transcript features such as novel exons and alternative splicing in RNA-Seq data from mouse retina. A pipeline based on BLAT was developed to explore the performance of established tools for this problem, and to compare it to the recently developed methods. This pipeline, the RNA-Seq Unified Mapper (RUM), performs comparably to the best current aligners and provides an advantageous combination of accuracy, speed and usability. AVAILABILITY: The RUM pipeline is distributed via the Amazon Cloud and for computing clusters using the Sun Grid Engine (http://cbil.upenn.edu/RUM). CONTACT: ggrant@pcbi.upenn.edu; epierce@mail.med.upenn.edu SUPPLEMENTARY INFORMATION: The RNA-Seq sequence reads described in the article are deposited at GEO, accession GSE26248.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.