ArticleBMC genomics2014
Comparing reference-based RNA-Seq mapping methods for non-human primate data.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
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- Current advances in primate genomics: novel approaches for understanding evolution and disease.Nature reviews. Genetics · 2023Review
- Bulk and Single-Cell RNA-Seq Analyses for Studies of Spermatogonia.Methods in molecular biology (Clifton, N.J.) · 2023Article
- The genome of a hadal sea cucumber reveals novel adaptive strategies to deep-sea environments.iScience · 2022Article
- Comparability of reference-based and reference-free transcriptome analysis approaches at the gene expression level.BMC bioinformatics · 2021Article
- RNA-Seq in Nonmodel Organisms.Methods in molecular biology (Clifton, N.J.) · 2021Article
- RNA-Seq Reveals Different Gene Expression in Liver-Specific Prohibitin 1 Knock-Out Mice.Frontiers in physiology · 2021Article
- Evaluation of Seven Different RNA-Seq Alignment Tools Based on Experimental Data from the Model PlantInternational journal of molecular sciences · 2020Article
- Conservation of cell-intrinsic immune responses in diverse nonhuman primate species.Life science alliance · 2019Article
- Comprehensive evaluation of RNA-seq analysis pipelines in diploid and polyploid species.GigaScience · 2018Article
- Understanding sequencing data as compositions: an outlook and review.Bioinformatics (Oxford, England) · 2018Review
- Benchmarking differential expression analysis tools for RNA-Seq: normalization-based vs. log-ratio transformation-based methods.BMC bioinformatics · 2018Article
- De novo assembling and primary analysis of genome and transcriptome of gray whale Eschrichtius robustus.BMC evolutionary biology · 2017Article
- Regulation of gene expression in roots of the pH-sensitive Vaccinium corymbosum and the pH-tolerant Vaccinium arboreum in response to near neutral pH stress using RNA-Seq.BMC genomics · 2017Article
- Simulation-based comprehensive benchmarking of RNA-seq aligners.Nature methods · 2017Article
- Empirical assessment of analysis workflows for differential expression analysis of human samples using RNA-Seq.BMC bioinformatics · 2017Article
- Article
- Selection of Optimal Bioinformatic Tools and Proper Reference for Reducing the Alignment Error in Targeted Sequencing Data.Journal of medical signals and sensorsArticle
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5 authors.
Funding
Abstract
backgroundThe application of next-generation sequencing technology to gene expression quantification analysis, namely, RNA-Sequencing, has transformed the way in which gene expression studies are conducted and analyzed. These advances are of particular interest to researchers studying organisms with missing or incomplete genomes, as the need for knowledge of sequence information is overcome. De novo assembly methods have gained widespread acceptance in the RNA-Seq community for organisms with no true reference genome or transcriptome. While such methods have tremendous utility, computational cost is still a significant challenge for organisms with large and complex genomes.
resultsIn this manuscript, we present a comparison of four reference-based mapping methods for non-human primate data. We utilize TopHat2 and GSNAP for mapping to the human genome, and Bowtie2 and Stampy for mapping to the human genome and transcriptome for a total of six mapping approaches. For each of these methods, we explore mapping rates and locations, number of detected genes, correlations between computed expression values, and the utility of the resulting data for differential expression analysis.
conclusionsWe show that reference-based mapping methods indeed have utility in RNA-Seq analysis of mammalian data with no true reference, and the details of mapping methods should be carefully considered when doing so. Critical algorithm features include short seed sequences, the allowance of mismatches, and the allowance of gapped alignments in addition to splice junction gaps. Such features facilitate sensitive alignment of non-human primate RNA-Seq data to a human reference.
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